PDB Short entry for 1JDE HEADER TRANSFERASE 13-JUN-01 1JDE TITLE K22A MUTANT OF PYRUVATE, PHOSPHATE DIKINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE, PHOSPHATE DIKINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPDK; COMPND 5 EC: 2.7.9.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM SYMBIOSUM; SOURCE 3 ORGANISM_TAXID: 1512; SOURCE 4 GENE: PODK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM 101; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PACYC184D-12 KEYWDS TRANSFERASE, PHOSPHOTRANSFERASE, KINASE, NUCLEOTIDE BINDING SITE KEYWDS 2 MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR D.YE,M.WEI,M.MCGUIRE,K.HUANG,G.KAPADIA,O.HERZBERG,B.M.MARTIN, AUTHOR 2 D.DUNAWAY-MARIANO REVDAT 7 07-FEB-24 1JDE 1 REMARK REVDAT 6 27-OCT-21 1JDE 1 REMARK SEQADV REVDAT 5 04-APR-18 1JDE 1 REMARK REVDAT 4 04-OCT-17 1JDE 1 REMARK REVDAT 3 13-JUL-11 1JDE 1 VERSN REVDAT 2 24-FEB-09 1JDE 1 VERSN REVDAT 1 28-NOV-01 1JDE 0 JRNL AUTH D.YE,M.WEI,M.MCGUIRE,K.HUANG,G.KAPADIA,O.HERZBERG, JRNL AUTH 2 B.M.MARTIN,D.DUNAWAY-MARIANO JRNL TITL INVESTIGATION OF THE CATALYTIC SITE WITHIN THE ATP-GRASP JRNL TITL 2 DOMAIN OF CLOSTRIDIUM SYMBIOSUM PYRUVATE PHOSPHATE DIKINASE. JRNL REF J.BIOL.CHEM. V. 276 37630 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11468288 JRNL DOI 10.1074/JBC.M105631200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.HERZBERG,C.C.CHEN,G.KAPADIA,M.MCGUIRE,L.J.CARROLL,S.J.NOH, REMARK 1 AUTH 2 D.DUNAWAY-MARIANO REMARK 1 TITL SWIVELING-DOMAIN MECHANISM FOR ENZYMATIC PHOSPHOTRANSFER REMARK 1 TITL 2 BETWEEN REMOTE REACTION SITES REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 93 2652 1996 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.93.7.2652 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 20093 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6717 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TNT WAS ALSO USED FOR REFINEMENT. REMARK 4 REMARK 4 1JDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013648. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-96 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25068 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1DIK WITHOUT SOLVENT MOLECULES AND WITH REMARK 200 K22 TRUNCATED TO GLY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% SATURATED AMMONIUM SULFATE, 100MM REMARK 280 HEPES BUFFER, 100MM KCL, 0.1MM EDTA, 1MM MERCAPTOETHANOL, 20MM REMARK 280 IMIDAZOLE BUFFER PH 6.5, 10MG/ML PROTEIN, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 66810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 89.90000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A 901 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ILE A 505 REMARK 465 TYR A 506 REMARK 465 LYS A 507 REMARK 465 GLY A 508 REMARK 465 ASP A 509 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLY A 278 N ASP A 280 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 28 CD GLU A 28 OE2 0.069 REMARK 500 GLU A 49 CD GLU A 49 OE2 0.073 REMARK 500 GLU A 60 CD GLU A 60 OE2 0.075 REMARK 500 GLU A 74 CD GLU A 74 OE2 0.076 REMARK 500 GLU A 84 CD GLU A 84 OE2 0.082 REMARK 500 GLU A 117 CD GLU A 117 OE2 0.068 REMARK 500 GLU A 146 CD GLU A 146 OE2 0.109 REMARK 500 GLU A 153 CD GLU A 153 OE2 0.098 REMARK 500 GLU A 162 CD GLU A 162 OE2 0.079 REMARK 500 GLU A 181 CD GLU A 181 OE2 0.079 REMARK 500 GLU A 194 CD GLU A 194 OE2 0.091 REMARK 500 GLU A 195 CD GLU A 195 OE2 0.082 REMARK 500 GLU A 249 CD GLU A 249 OE2 0.099 REMARK 500 GLU A 265 CD GLU A 265 OE2 0.072 REMARK 500 GLU A 271 CD GLU A 271 OE2 0.078 REMARK 500 GLU A 279 CD GLU A 279 OE2 0.074 REMARK 500 GLU A 323 CD GLU A 323 OE2 0.070 REMARK 500 GLU A 328 CD GLU A 328 OE2 0.078 REMARK 500 GLU A 362 CD GLU A 362 OE2 0.070 REMARK 500 GLU A 363 CD GLU A 363 OE2 0.067 REMARK 500 GLU A 390 CD GLU A 390 OE2 0.088 REMARK 500 GLU A 419 CD GLU A 419 OE2 0.096 REMARK 500 GLU A 422 CD GLU A 422 OE2 0.086 REMARK 500 GLU A 434 CD GLU A 434 OE2 0.070 REMARK 500 GLU A 437 CD GLU A 437 OE2 0.069 REMARK 500 GLU A 479 CD GLU A 479 OE2 0.071 REMARK 500 GLU A 484 CD GLU A 484 OE2 0.075 REMARK 500 GLU A 511 CD GLU A 511 OE2 0.076 REMARK 500 GLU A 514 CD GLU A 514 OE2 0.081 REMARK 500 GLU A 522 CD GLU A 522 OE2 0.083 REMARK 500 GLU A 544 CD GLU A 544 OE2 0.071 REMARK 500 GLU A 610 CD GLU A 610 OE2 0.080 REMARK 500 GLU A 625 CD GLU A 625 OE2 0.085 REMARK 500 GLU A 632 CD GLU A 632 OE2 0.068 REMARK 500 GLU A 633 CD GLU A 633 OE2 0.080 REMARK 500 GLU A 647 CD GLU A 647 OE2 0.068 REMARK 500 GLU A 675 CD GLU A 675 OE2 0.075 REMARK 500 GLU A 694 CD GLU A 694 OE2 0.103 REMARK 500 GLU A 702 CD GLU A 702 OE2 0.092 REMARK 500 GLU A 710 CD GLU A 710 OE2 0.093 REMARK 500 GLU A 723 CD GLU A 723 OE2 0.088 REMARK 500 GLU A 726 CD GLU A 726 OE2 0.090 REMARK 500 GLU A 758 CD GLU A 758 OE2 0.077 REMARK 500 GLU A 759 CD GLU A 759 OE2 0.086 REMARK 500 GLU A 761 CD GLU A 761 OE2 0.071 REMARK 500 GLU A 796 CD GLU A 796 OE2 0.088 REMARK 500 GLU A 813 CD GLU A 813 OE2 0.068 REMARK 500 GLU A 833 CD GLU A 833 OE2 0.066 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 63 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ASP A 131 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP A 142 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ASP A 168 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 168 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 170 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 PRO A 197 C - N - CA ANGL. DEV. = 10.3 DEGREES REMARK 500 PRO A 197 C - N - CD ANGL. DEV. = -32.1 DEGREES REMARK 500 ASP A 202 CB - CG - OD2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ASP A 216 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 216 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 224 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 VAL A 243 CB - CA - C ANGL. DEV. = 11.5 DEGREES REMARK 500 ARG A 259 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 259 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 280 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 280 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 PRO A 299 C - N - CD ANGL. DEV. = -14.3 DEGREES REMARK 500 ASP A 321 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 337 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 CYS A 351 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 355 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ALA A 384 N - CA - CB ANGL. DEV. = 9.3 DEGREES REMARK 500 ASP A 412 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 449 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP A 529 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 537 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 541 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ASP A 570 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP A 582 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 601 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 601 CB - CG - OD2 ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG A 617 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 617 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 620 CB - CG - OD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ASP A 653 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 665 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 665 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 668 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 668 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 682 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ASP A 719 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ASP A 719 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ASP A 754 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 781 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 798 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 798 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ASP A 804 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 837 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 10 34.58 -97.77 REMARK 500 ASN A 12 -173.33 -172.49 REMARK 500 MET A 15 22.68 -65.89 REMARK 500 ALA A 22 -76.03 -71.03 REMARK 500 PRO A 35 55.80 -66.25 REMARK 500 GLN A 38 166.75 -41.72 REMARK 500 ASN A 52 39.56 -67.84 REMARK 500 SER A 53 -22.39 -162.33 REMARK 500 LYS A 55 31.42 144.56 REMARK 500 GLN A 59 -124.27 -7.79 REMARK 500 GLU A 60 -36.48 -20.80 REMARK 500 LEU A 72 -78.69 -54.17 REMARK 500 GLU A 73 -61.00 -18.53 REMARK 500 GLU A 74 -71.90 -63.48 REMARK 500 LEU A 75 -31.00 -34.43 REMARK 500 PHE A 80 92.28 -58.81 REMARK 500 GLU A 84 -61.05 -96.84 REMARK 500 PRO A 86 -171.45 -66.92 REMARK 500 ALA A 95 -178.34 -62.93 REMARK 500 ARG A 96 -93.19 -59.15 REMARK 500 MET A 99 52.72 -157.53 REMARK 500 ASN A 108 59.44 11.93 REMARK 500 ASN A 125 85.61 175.84 REMARK 500 PHE A 128 -78.73 -67.21 REMARK 500 MET A 139 -80.44 -41.26 REMARK 500 TYR A 140 -53.82 -28.25 REMARK 500 VAL A 144 12.07 -66.04 REMARK 500 MET A 145 106.82 28.24 REMARK 500 GLU A 146 -7.12 -145.76 REMARK 500 LYS A 149 -39.70 -35.87 REMARK 500 SER A 150 -47.74 -26.26 REMARK 500 HIS A 151 -85.11 -60.52 REMARK 500 GLU A 161 46.73 -78.03 REMARK 500 GLU A 162 -25.49 -176.17 REMARK 500 VAL A 165 116.07 -21.05 REMARK 500 THR A 169 -18.90 -47.28 REMARK 500 LEU A 176 -73.27 -52.11 REMARK 500 LEU A 179 -72.82 -50.91 REMARK 500 ALA A 180 11.33 -60.65 REMARK 500 PHE A 196 97.93 -53.01 REMARK 500 PRO A 197 66.29 -9.01 REMARK 500 LYS A 201 40.30 -84.48 REMARK 500 ASP A 202 -27.67 -155.88 REMARK 500 LEU A 204 -75.94 -43.76 REMARK 500 VAL A 211 -73.45 -102.35 REMARK 500 PHE A 212 19.73 -53.85 REMARK 500 ARG A 213 -19.10 -147.79 REMARK 500 TRP A 215 -56.10 -25.87 REMARK 500 ASP A 216 13.39 -69.93 REMARK 500 PRO A 218 -70.41 -26.78 REMARK 500 REMARK 500 THIS ENTRY HAS 143 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DIK RELATED DB: PDB REMARK 900 WILD-TYPE PYRUVATE PHOSPHATE DIKINASE REMARK 900 RELATED ID: 2DIK RELATED DB: PDB REMARK 900 R337A MUTANT OF PYRUVATE PHOSPHATE DIKINASE REMARK 900 RELATED ID: 1GGO RELATED DB: PDB REMARK 900 T453A MUTANT OF PYRUVATE PHOSPHATE DIKINASE DBREF 1JDE A 2 874 UNP P22983 PPDK_CLOSY 1 873 SEQADV 1JDE ALA A 22 UNP P22983 LYS 21 ENGINEERED MUTATION SEQRES 1 A 873 ALA LYS TRP VAL TYR LYS PHE GLU GLU GLY ASN ALA SER SEQRES 2 A 873 MET ARG ASN LEU LEU GLY GLY ALA GLY CYS ASN LEU ALA SEQRES 3 A 873 GLU MET THR ILE LEU GLY MET PRO ILE PRO GLN GLY PHE SEQRES 4 A 873 THR VAL THR THR GLU ALA CYS THR GLU TYR TYR ASN SER SEQRES 5 A 873 GLY LYS GLN ILE THR GLN GLU ILE GLN ASP GLN ILE PHE SEQRES 6 A 873 GLU ALA ILE THR TRP LEU GLU GLU LEU ASN GLY LYS LYS SEQRES 7 A 873 PHE GLY ASP THR GLU ASP PRO LEU LEU VAL SER VAL ARG SEQRES 8 A 873 SER GLY ALA ARG ALA SER MET PRO GLY MET MET ASP THR SEQRES 9 A 873 ILE LEU ASN LEU GLY LEU ASN ASP VAL ALA VAL GLU GLY SEQRES 10 A 873 PHE ALA LYS LYS THR GLY ASN PRO ARG PHE ALA TYR ASP SEQRES 11 A 873 SER TYR ARG ARG PHE ILE GLN MET TYR SER ASP VAL VAL SEQRES 12 A 873 MET GLU VAL PRO LYS SER HIS PHE GLU LYS ILE ILE ASP SEQRES 13 A 873 ALA MET LYS GLU GLU LYS GLY VAL HIS PHE ASP THR ASP SEQRES 14 A 873 LEU THR ALA ASP ASP LEU LYS GLU LEU ALA GLU LYS PHE SEQRES 15 A 873 LYS ALA VAL TYR LYS GLU ALA MET ASN GLY GLU GLU PHE SEQRES 16 A 873 PRO GLN GLU PRO LYS ASP GLN LEU MET GLY ALA VAL LYS SEQRES 17 A 873 ALA VAL PHE ARG SER TRP ASP ASN PRO ARG ALA ILE VAL SEQRES 18 A 873 TYR ARG ARG MET ASN ASP ILE PRO GLY ASP TRP GLY THR SEQRES 19 A 873 ALA VAL ASN VAL GLN THR MET VAL PHE GLY ASN LYS GLY SEQRES 20 A 873 GLU THR SER GLY THR GLY VAL ALA PHE THR ARG ASN PRO SEQRES 21 A 873 SER THR GLY GLU LYS GLY ILE TYR GLY GLU TYR LEU ILE SEQRES 22 A 873 ASN ALA GLN GLY GLU ASP VAL VAL ALA GLY VAL ARG THR SEQRES 23 A 873 PRO GLN PRO ILE THR GLN LEU GLU ASN ASP MET PRO ASP SEQRES 24 A 873 CYS TYR LYS GLN PHE MET ASP LEU ALA MET LYS LEU GLU SEQRES 25 A 873 LYS HIS PHE ARG ASP MET GLN ASP MET GLU PHE THR ILE SEQRES 26 A 873 GLU GLU GLY LYS LEU TYR PHE LEU GLN THR ARG ASN GLY SEQRES 27 A 873 LYS ARG THR ALA PRO ALA ALA LEU GLN ILE ALA CYS ASP SEQRES 28 A 873 LEU VAL ASP GLU GLY MET ILE THR GLU GLU GLU ALA VAL SEQRES 29 A 873 VAL ARG ILE GLU ALA LYS SER LEU ASP GLN LEU LEU HIS SEQRES 30 A 873 PRO THR PHE ASN PRO ALA ALA LEU LYS ALA GLY GLU VAL SEQRES 31 A 873 ILE GLY SER ALA LEU PRO ALA SER PRO GLY ALA ALA ALA SEQRES 32 A 873 GLY LYS VAL TYR PHE THR ALA ASP GLU ALA LYS ALA ALA SEQRES 33 A 873 HIS GLU LYS GLY GLU ARG VAL ILE LEU VAL ARG LEU GLU SEQRES 34 A 873 THR SER PRO GLU ASP ILE GLU GLY MET HIS ALA ALA GLU SEQRES 35 A 873 GLY ILE LEU THR VAL ARG GLY GLY MET THR SER HIS ALA SEQRES 36 A 873 ALA VAL VAL ALA ARG GLY MET GLY THR CYS CYS VAL SER SEQRES 37 A 873 GLY CYS GLY GLU ILE LYS ILE ASN GLU GLU ALA LYS THR SEQRES 38 A 873 PHE GLU LEU GLY GLY HIS THR PHE ALA GLU GLY ASP TYR SEQRES 39 A 873 ILE SER LEU ASP GLY SER THR GLY LYS ILE TYR LYS GLY SEQRES 40 A 873 ASP ILE GLU THR GLN GLU ALA SER VAL SER GLY SER PHE SEQRES 41 A 873 GLU ARG ILE MET VAL TRP ALA ASP LYS PHE ARG THR LEU SEQRES 42 A 873 LYS VAL ARG THR ASN ALA ASP THR PRO GLU ASP THR LEU SEQRES 43 A 873 ASN ALA VAL LYS LEU GLY ALA GLU GLY ILE GLY LEU CYS SEQRES 44 A 873 ARG THR GLU HIS MET PHE PHE GLU ALA ASP ARG ILE MET SEQRES 45 A 873 LYS ILE ARG LYS MET ILE LEU SER ASP SER VAL GLU ALA SEQRES 46 A 873 ARG GLU GLU ALA LEU ASN GLU LEU ILE PRO PHE GLN LYS SEQRES 47 A 873 GLY ASP PHE LYS ALA MET TYR LYS ALA LEU GLU GLY ARG SEQRES 48 A 873 PRO MET THR VAL ARG TYR LEU ASP PRO PRO LEU HIS GLU SEQRES 49 A 873 PHE VAL PRO HIS THR GLU GLU GLU GLN ALA GLU LEU ALA SEQRES 50 A 873 LYS ASN MET GLY LEU THR LEU ALA GLU VAL LYS ALA LYS SEQRES 51 A 873 VAL ASP GLU LEU HIS GLU PHE ASN PRO MET MET GLY HIS SEQRES 52 A 873 ARG GLY CYS ARG LEU ALA VAL THR TYR PRO GLU ILE ALA SEQRES 53 A 873 LYS MET GLN THR ARG ALA VAL MET GLU ALA ALA ILE GLU SEQRES 54 A 873 VAL LYS GLU GLU THR GLY ILE ASP ILE VAL PRO GLU ILE SEQRES 55 A 873 MET ILE PRO LEU VAL GLY GLU LYS LYS GLU LEU LYS PHE SEQRES 56 A 873 VAL LYS ASP VAL VAL VAL GLU VAL ALA GLU GLN VAL LYS SEQRES 57 A 873 LYS GLU LYS GLY SER ASP MET GLN TYR HIS ILE GLY THR SEQRES 58 A 873 MET ILE GLU ILE PRO ARG ALA ALA LEU THR ALA ASP ALA SEQRES 59 A 873 ILE ALA GLU GLU ALA GLU PHE PHE SER PHE GLY THR ASN SEQRES 60 A 873 ASP LEU THR GLN MET THR PHE GLY PHE SER ARG ASP ASP SEQRES 61 A 873 ALA GLY LYS PHE LEU ASP SER TYR TYR LYS ALA LYS ILE SEQRES 62 A 873 TYR GLU SER ASP PRO PHE ALA ARG LEU ASP GLN THR GLY SEQRES 63 A 873 VAL GLY GLN LEU VAL GLU MET ALA VAL LYS LYS GLY ARG SEQRES 64 A 873 GLN THR ARG PRO GLY LEU LYS CYS GLY ILE CYS GLY GLU SEQRES 65 A 873 HIS GLY GLY ASP PRO SER SER VAL GLU PHE CYS HIS LYS SEQRES 66 A 873 VAL GLY LEU ASN TYR VAL SER CYS SER PRO PHE ARG VAL SEQRES 67 A 873 PRO ILE ALA ARG LEU ALA ALA ALA GLN ALA ALA LEU ASN SEQRES 68 A 873 ASN LYS HET SO4 A 901 5 HET SO4 A 902 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *41(H2 O) HELIX 1 1 MET A 15 GLY A 20 1 6 HELIX 2 2 GLY A 20 GLY A 33 1 14 HELIX 3 3 THR A 43 ASN A 52 1 10 HELIX 4 4 THR A 58 ALA A 68 1 11 HELIX 5 5 ALA A 68 ASN A 76 1 9 HELIX 6 6 ASN A 112 THR A 123 1 12 HELIX 7 7 ASN A 125 VAL A 144 1 20 HELIX 8 8 LYS A 149 GLU A 161 1 13 HELIX 9 9 PHE A 167 LEU A 171 5 5 HELIX 10 10 THR A 172 MET A 191 1 20 HELIX 11 11 GLU A 199 PHE A 212 1 14 HELIX 12 12 ASN A 217 ASN A 227 1 11 HELIX 13 13 GLN A 277 VAL A 282 1 6 HELIX 14 14 GLN A 293 MET A 298 1 6 HELIX 15 15 ASP A 300 ARG A 317 1 18 HELIX 16 16 THR A 342 GLU A 356 1 15 HELIX 17 17 THR A 360 ARG A 367 1 8 HELIX 18 18 GLU A 369 HIS A 378 5 10 HELIX 19 19 ASN A 382 LYS A 387 1 6 HELIX 20 20 THR A 410 ALA A 416 1 7 HELIX 21 21 SER A 432 GLU A 434 5 3 HELIX 22 22 ASP A 435 HIS A 440 1 6 HELIX 23 23 SER A 454 GLY A 464 1 11 HELIX 24 24 SER A 518 ARG A 532 1 15 HELIX 25 25 THR A 542 LEU A 552 1 11 HELIX 26 26 GLU A 563 GLU A 568 1 6 HELIX 27 27 ARG A 571 MET A 573 5 3 HELIX 28 28 LYS A 574 ILE A 579 1 6 HELIX 29 29 SER A 583 GLU A 610 1 28 HELIX 30 30 PRO A 622 VAL A 627 5 6 HELIX 31 31 GLU A 631 ASN A 640 1 10 HELIX 32 32 THR A 644 GLU A 654 1 11 HELIX 33 33 CYS A 667 VAL A 671 5 5 HELIX 34 34 TYR A 673 GLU A 694 1 22 HELIX 35 35 GLU A 710 LYS A 729 1 20 HELIX 36 36 ILE A 746 THR A 752 1 7 HELIX 37 37 THR A 752 ALA A 757 1 6 HELIX 38 38 THR A 767 GLY A 776 1 10 HELIX 39 39 ALA A 782 ALA A 792 1 11 HELIX 40 40 GLY A 807 ARG A 823 1 17 HELIX 41 41 GLY A 832 GLY A 836 5 5 HELIX 42 42 SER A 839 GLY A 848 1 10 HELIX 43 43 ARG A 858 LYS A 874 1 17 SHEET 1 A 5 TYR A 6 LYS A 7 0 SHEET 2 A 5 GLY A 39 VAL A 42 -1 O THR A 41 N TYR A 6 SHEET 3 A 5 VAL A 237 THR A 241 -1 O VAL A 237 N VAL A 42 SHEET 4 A 5 VAL A 89 SER A 93 -1 N SER A 90 O GLN A 240 SHEET 5 A 5 THR A 105 LEU A 109 -1 N ILE A 106 O VAL A 91 SHEET 1 B 5 GLN A 289 PRO A 290 0 SHEET 2 B 5 LYS A 266 ILE A 274 -1 N TYR A 272 O GLN A 289 SHEET 3 B 5 GLY A 252 ARG A 259 -1 N THR A 253 O LEU A 273 SHEET 4 B 5 ASP A 321 ILE A 326 -1 O MET A 322 N ALA A 256 SHEET 5 B 5 LEU A 331 GLN A 335 -1 N TYR A 332 O THR A 325 SHEET 1 C 2 THR A 380 PHE A 381 0 SHEET 2 C 2 THR A 512 GLN A 513 -1 O GLN A 513 N THR A 380 SHEET 1 D 6 CYS A 466 VAL A 468 0 SHEET 2 D 6 GLY A 444 THR A 447 1 O ILE A 445 N VAL A 468 SHEET 3 D 6 VAL A 424 ARG A 428 1 O VAL A 424 N GLY A 444 SHEET 4 D 6 ALA A 404 TYR A 408 1 O LYS A 406 N ILE A 425 SHEET 5 D 6 TYR A 495 SER A 497 -1 N TYR A 495 O GLY A 405 SHEET 6 D 6 GLY A 503 LYS A 504 -1 O LYS A 504 N ILE A 496 SHEET 1 E 2 GLU A 484 LEU A 485 0 SHEET 2 E 2 HIS A 488 THR A 489 -1 N HIS A 488 O LEU A 485 SHEET 1 F 7 THR A 538 ALA A 540 0 SHEET 2 F 7 ILE A 557 CYS A 560 1 N GLY A 558 O THR A 538 SHEET 3 F 7 MET A 614 ARG A 617 1 N THR A 615 O ILE A 557 SHEET 4 F 7 GLU A 702 ILE A 705 1 O GLU A 702 N VAL A 616 SHEET 5 F 7 HIS A 739 MET A 743 1 O HIS A 739 N ILE A 703 SHEET 6 F 7 PHE A 762 PHE A 765 1 O PHE A 762 N THR A 742 SHEET 7 F 7 LYS A 827 ILE A 830 1 O LYS A 827 N PHE A 763 SITE 1 AC1 3 GLU A 361 ARG A 523 TRP A 527 SITE 1 AC2 6 MET A 99 PRO A 100 GLY A 101 MET A 102 SITE 2 AC2 6 MET A 103 ARG A 337 CRYST1 89.900 58.600 102.300 90.00 95.10 90.00 P 1 2 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011123 0.000000 0.000993 0.00000 SCALE2 0.000000 0.017065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009814 0.00000