PDB Short entry for 2ZYA HEADER OXIDOREDUCTASE 19-JAN-09 2ZYA TITLE DIMERIC 6-PHOSPHOGLUCONATE DEHYDROGENASE COMPLEXED WITH 6- TITLE 2 PHOSPHOGLUCONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.1.44; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: SPECIFIC MUTATION Y378C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: GND; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS NADP, PENTOSE PHOSPHATE PATHWAY, OXIDOREDUCTASE, 6-PHOSPHOGLUCONATE KEYWDS 2 DEHYDROGENASE, 6-PHOSPHOGLUCONATE, GLUCONATE UTILIZATION, PENTOSE KEYWDS 3 SHUNT EXPDTA X-RAY DIFFRACTION AUTHOR Y.-Y.CHEN,T.-P.KO,L.-P.LO,C.-H.LIN,A.H.-J.WANG REVDAT 6 01-NOV-23 2ZYA 1 REMARK REVDAT 5 10-NOV-21 2ZYA 1 SEQADV REVDAT 4 11-OCT-17 2ZYA 1 REMARK REVDAT 3 22-JAN-14 2ZYA 1 JRNL REVDAT 2 13-JUL-11 2ZYA 1 VERSN REVDAT 1 01-SEP-09 2ZYA 0 JRNL AUTH Y.-Y.CHEN,T.-P.KO,W.-H.CHEN,L.-P.LO,C.-H.LIN,A.H.-J.WANG JRNL TITL CONFORMATIONAL CHANGES ASSOCIATED WITH COFACTOR/SUBSTRATE JRNL TITL 2 BINDING OF 6-PHOSPHOGLUCONATE DEHYDROGENASE FROM ESCHERICHIA JRNL TITL 3 COLI AND KLEBSIELLA PNEUMONIAE: IMPLICATIONS FOR ENZYME JRNL TITL 4 MECHANISM JRNL REF J.STRUCT.BIOL. V. 169 25 2010 JRNL REFN ISSN 1047-8477 JRNL PMID 19686854 JRNL DOI 10.1016/J.JSB.2009.08.006 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 116335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 6192 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.42 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2049 REMARK 3 BIN FREE R VALUE : 0.2314 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 582 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7212 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 1397 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) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.776 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: NULL REMARK 4 REMARK 4 2ZYA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000028577. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 126816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 6.120 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.56 REMARK 200 R MERGE FOR SHELL (I) : 0.49500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1PGP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRISODIUM CITRATE DIHRDRATE, 0.5M REMARK 280 AMMONIUM ACETATE, 6-7% PEG 3350, 17-18% PEG 4000, 3MM 6- REMARK 280 PHOSPHOGLUCONATE, PH 5.4, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 34.00200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.75250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.35900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.75250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.00200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.35900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: 11840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 MET A -11 REMARK 465 GLY A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LEU A 467 REMARK 465 ASP A 468 REMARK 465 MET B -11 REMARK 465 GLY B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ASP B 468 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 HOH A 593 O HOH B 705 2.07 REMARK 500 OE2 GLU B 316 O HOH B 1265 2.13 REMARK 500 O HOH B 563 O HOH B 1102 2.14 REMARK 500 OD2 ASP B 251 O HOH B 1067 2.15 REMARK 500 OE2 GLU A 345 O HOH A 814 2.16 REMARK 500 O HOH B 722 O HOH B 1156 2.16 REMARK 500 O HOH A 498 O HOH A 910 2.17 REMARK 500 O HOH B 679 O HOH B 1239 2.17 REMARK 500 O HOH A 802 O HOH B 707 2.18 REMARK 500 O HOH B 587 O HOH B 1272 2.18 REMARK 500 O HOH A 693 O HOH B 975 2.18 REMARK 500 O HOH A 491 O HOH A 1283 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 678 O HOH B 948 2564 2.18 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 GLY A 263 C GLY A 263 O 0.157 REMARK 500 GLY B 263 C GLY B 263 O 0.160 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 GLY A 261 N - CA - C ANGL. DEV. = 16.1 DEGREES REMARK 500 MET B 141 CG - SD - CE ANGL. DEV. = -13.4 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 ALA A 12 -179.08 -65.35 REMARK 500 ASP A 176 -113.24 37.77 REMARK 500 ASP A 245 3.33 -57.07 REMARK 500 LEU A 292 49.56 -100.00 REMARK 500 THR A 452 159.15 68.74 REMARK 500 ASP B 176 -112.68 38.88 REMARK 500 SER B 228 119.10 -34.49 REMARK 500 LEU B 292 50.50 -95.05 REMARK 500 THR B 452 159.77 71.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 427 0.07 SIDE CHAIN REMARK 500 TYR B 353 0.08 SIDE CHAIN 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 6PG A2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 6PG B2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZYD RELATED DB: PDB REMARK 900 RELATED ENTRY DESCRIPTION MODEL FOR MOLECULAR REPLACEMENT REMARK 900 RELATED ID: 3FWN RELATED DB: PDB REMARK 900 RELATED ID: 2ZYG RELATED DB: PDB DBREF 2ZYA A 1 468 UNP P00350 6PGD_ECOLI 1 468 DBREF 2ZYA B 1 468 UNP P00350 6PGD_ECOLI 1 468 SEQADV 2ZYA MET A -11 UNP P00350 EXPRESSION TAG SEQADV 2ZYA GLY A -10 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS A -9 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS A -8 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS A -7 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS A -6 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS A -5 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS A -4 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS A -3 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS A -2 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS A -1 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS A 0 UNP P00350 EXPRESSION TAG SEQADV 2ZYA CYS A 378 UNP P00350 TYR 378 ENGINEERED MUTATION SEQADV 2ZYA MET B -11 UNP P00350 EXPRESSION TAG SEQADV 2ZYA GLY B -10 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS B -9 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS B -8 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS B -7 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS B -6 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS B -5 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS B -4 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS B -3 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS B -2 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS B -1 UNP P00350 EXPRESSION TAG SEQADV 2ZYA HIS B 0 UNP P00350 EXPRESSION TAG SEQADV 2ZYA CYS B 378 UNP P00350 TYR 378 ENGINEERED MUTATION SEQRES 1 A 480 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS MET SEQRES 2 A 480 SER LYS GLN GLN ILE GLY VAL VAL GLY MET ALA VAL MET SEQRES 3 A 480 GLY ARG ASN LEU ALA LEU ASN ILE GLU SER ARG GLY TYR SEQRES 4 A 480 THR VAL SER ILE PHE ASN ARG SER ARG GLU LYS THR GLU SEQRES 5 A 480 GLU VAL ILE ALA GLU ASN PRO GLY LYS LYS LEU VAL PRO SEQRES 6 A 480 TYR TYR THR VAL LYS GLU PHE VAL GLU SER LEU GLU THR SEQRES 7 A 480 PRO ARG ARG ILE LEU LEU MET VAL LYS ALA GLY ALA GLY SEQRES 8 A 480 THR ASP ALA ALA ILE ASP SER LEU LYS PRO TYR LEU ASP SEQRES 9 A 480 LYS GLY ASP ILE ILE ILE ASP GLY GLY ASN THR PHE PHE SEQRES 10 A 480 GLN ASP THR ILE ARG ARG ASN ARG GLU LEU SER ALA GLU SEQRES 11 A 480 GLY PHE ASN PHE ILE GLY THR GLY VAL SER GLY GLY GLU SEQRES 12 A 480 GLU GLY ALA LEU LYS GLY PRO SER ILE MET PRO GLY GLY SEQRES 13 A 480 GLN LYS GLU ALA TYR GLU LEU VAL ALA PRO ILE LEU THR SEQRES 14 A 480 LYS ILE ALA ALA VAL ALA GLU ASP GLY GLU PRO CYS VAL SEQRES 15 A 480 THR TYR ILE GLY ALA ASP GLY ALA GLY HIS TYR VAL LYS SEQRES 16 A 480 MET VAL HIS ASN GLY ILE GLU TYR GLY ASP MET GLN LEU SEQRES 17 A 480 ILE ALA GLU ALA TYR SER LEU LEU LYS GLY GLY LEU ASN SEQRES 18 A 480 LEU THR ASN GLU GLU LEU ALA GLN THR PHE THR GLU TRP SEQRES 19 A 480 ASN ASN GLY GLU LEU SER SER TYR LEU ILE ASP ILE THR SEQRES 20 A 480 LYS ASP ILE PHE THR LYS LYS ASP GLU ASP GLY ASN TYR SEQRES 21 A 480 LEU VAL ASP VAL ILE LEU ASP GLU ALA ALA ASN LYS GLY SEQRES 22 A 480 THR GLY LYS TRP THR SER GLN SER ALA LEU ASP LEU GLY SEQRES 23 A 480 GLU PRO LEU SER LEU ILE THR GLU SER VAL PHE ALA ARG SEQRES 24 A 480 TYR ILE SER SER LEU LYS ASP GLN ARG VAL ALA ALA SER SEQRES 25 A 480 LYS VAL LEU SER GLY PRO GLN ALA GLN PRO ALA GLY ASP SEQRES 26 A 480 LYS ALA GLU PHE ILE GLU LYS VAL ARG ARG ALA LEU TYR SEQRES 27 A 480 LEU GLY LYS ILE VAL SER TYR ALA GLN GLY PHE SER GLN SEQRES 28 A 480 LEU ARG ALA ALA SER GLU GLU TYR ASN TRP ASP LEU ASN SEQRES 29 A 480 TYR GLY GLU ILE ALA LYS ILE PHE ARG ALA GLY CYS ILE SEQRES 30 A 480 ILE ARG ALA GLN PHE LEU GLN LYS ILE THR ASP ALA CYS SEQRES 31 A 480 ALA GLU ASN PRO GLN ILE ALA ASN LEU LEU LEU ALA PRO SEQRES 32 A 480 TYR PHE LYS GLN ILE ALA ASP ASP TYR GLN GLN ALA LEU SEQRES 33 A 480 ARG ASP VAL VAL ALA TYR ALA VAL GLN ASN GLY ILE PRO SEQRES 34 A 480 VAL PRO THR PHE SER ALA ALA VAL ALA TYR TYR ASP SER SEQRES 35 A 480 TYR ARG ALA ALA VAL LEU PRO ALA ASN LEU ILE GLN ALA SEQRES 36 A 480 GLN ARG ASP TYR PHE GLY ALA HIS THR TYR LYS ARG ILE SEQRES 37 A 480 ASP LYS GLU GLY VAL PHE HIS THR GLU TRP LEU ASP SEQRES 1 B 480 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS MET SEQRES 2 B 480 SER LYS GLN GLN ILE GLY VAL VAL GLY MET ALA VAL MET SEQRES 3 B 480 GLY ARG ASN LEU ALA LEU ASN ILE GLU SER ARG GLY TYR SEQRES 4 B 480 THR VAL SER ILE PHE ASN ARG SER ARG GLU LYS THR GLU SEQRES 5 B 480 GLU VAL ILE ALA GLU ASN PRO GLY LYS LYS LEU VAL PRO SEQRES 6 B 480 TYR TYR THR VAL LYS GLU PHE VAL GLU SER LEU GLU THR SEQRES 7 B 480 PRO ARG ARG ILE LEU LEU MET VAL LYS ALA GLY ALA GLY SEQRES 8 B 480 THR ASP ALA ALA ILE ASP SER LEU LYS PRO TYR LEU ASP SEQRES 9 B 480 LYS GLY ASP ILE ILE ILE ASP GLY GLY ASN THR PHE PHE SEQRES 10 B 480 GLN ASP THR ILE ARG ARG ASN ARG GLU LEU SER ALA GLU SEQRES 11 B 480 GLY PHE ASN PHE ILE GLY THR GLY VAL SER GLY GLY GLU SEQRES 12 B 480 GLU GLY ALA LEU LYS GLY PRO SER ILE MET PRO GLY GLY SEQRES 13 B 480 GLN LYS GLU ALA TYR GLU LEU VAL ALA PRO ILE LEU THR SEQRES 14 B 480 LYS ILE ALA ALA VAL ALA GLU ASP GLY GLU PRO CYS VAL SEQRES 15 B 480 THR TYR ILE GLY ALA ASP GLY ALA GLY HIS TYR VAL LYS SEQRES 16 B 480 MET VAL HIS ASN GLY ILE GLU TYR GLY ASP MET GLN LEU SEQRES 17 B 480 ILE ALA GLU ALA TYR SER LEU LEU LYS GLY GLY LEU ASN SEQRES 18 B 480 LEU THR ASN GLU GLU LEU ALA GLN THR PHE THR GLU TRP SEQRES 19 B 480 ASN ASN GLY GLU LEU SER SER TYR LEU ILE ASP ILE THR SEQRES 20 B 480 LYS ASP ILE PHE THR LYS LYS ASP GLU ASP GLY ASN TYR SEQRES 21 B 480 LEU VAL ASP VAL ILE LEU ASP GLU ALA ALA ASN LYS GLY SEQRES 22 B 480 THR GLY LYS TRP THR SER GLN SER ALA LEU ASP LEU GLY SEQRES 23 B 480 GLU PRO LEU SER LEU ILE THR GLU SER VAL PHE ALA ARG SEQRES 24 B 480 TYR ILE SER SER LEU LYS ASP GLN ARG VAL ALA ALA SER SEQRES 25 B 480 LYS VAL LEU SER GLY PRO GLN ALA GLN PRO ALA GLY ASP SEQRES 26 B 480 LYS ALA GLU PHE ILE GLU LYS VAL ARG ARG ALA LEU TYR SEQRES 27 B 480 LEU GLY LYS ILE VAL SER TYR ALA GLN GLY PHE SER GLN SEQRES 28 B 480 LEU ARG ALA ALA SER GLU GLU TYR ASN TRP ASP LEU ASN SEQRES 29 B 480 TYR GLY GLU ILE ALA LYS ILE PHE ARG ALA GLY CYS ILE SEQRES 30 B 480 ILE ARG ALA GLN PHE LEU GLN LYS ILE THR ASP ALA CYS SEQRES 31 B 480 ALA GLU ASN PRO GLN ILE ALA ASN LEU LEU LEU ALA PRO SEQRES 32 B 480 TYR PHE LYS GLN ILE ALA ASP ASP TYR GLN GLN ALA LEU SEQRES 33 B 480 ARG ASP VAL VAL ALA TYR ALA VAL GLN ASN GLY ILE PRO SEQRES 34 B 480 VAL PRO THR PHE SER ALA ALA VAL ALA TYR TYR ASP SER SEQRES 35 B 480 TYR ARG ALA ALA VAL LEU PRO ALA ASN LEU ILE GLN ALA SEQRES 36 B 480 GLN ARG ASP TYR PHE GLY ALA HIS THR TYR LYS ARG ILE SEQRES 37 B 480 ASP LYS GLU GLY VAL PHE HIS THR GLU TRP LEU ASP HET 6PG A2002 17 HET 6PG B2001 17 HETNAM 6PG 6-PHOSPHOGLUCONIC ACID FORMUL 3 6PG 2(C6 H13 O10 P) FORMUL 5 HOH *1397(H2 O) HELIX 1 1 ALA A 12 ARG A 25 1 14 HELIX 2 2 SER A 35 ASN A 46 1 12 HELIX 3 3 THR A 56 SER A 63 1 8 HELIX 4 4 GLY A 77 LYS A 88 1 12 HELIX 5 5 PRO A 89 LEU A 91 5 3 HELIX 6 6 PHE A 104 GLU A 118 1 15 HELIX 7 7 GLY A 129 GLY A 137 1 9 HELIX 8 8 GLN A 145 ALA A 160 1 16 HELIX 9 9 GLY A 177 ASN A 209 1 33 HELIX 10 10 THR A 211 GLY A 225 1 15 HELIX 11 11 SER A 229 PHE A 239 1 11 HELIX 12 12 TYR A 248 ILE A 253 5 6 HELIX 13 13 GLY A 261 GLY A 274 1 14 HELIX 14 14 LEU A 277 SER A 291 1 15 HELIX 15 15 LEU A 292 LYS A 301 1 10 HELIX 16 16 ASP A 313 ASN A 348 1 36 HELIX 17 17 ASN A 352 PHE A 360 1 9 HELIX 18 18 GLN A 369 ASN A 381 1 13 HELIX 19 19 ASN A 386 LEU A 389 5 4 HELIX 20 20 ALA A 390 GLY A 415 1 26 HELIX 21 21 VAL A 418 ARG A 432 1 15 HELIX 22 22 PRO A 437 ALA A 450 1 14 HELIX 23 23 ALA B 12 ARG B 25 1 14 HELIX 24 24 SER B 35 ASN B 46 1 12 HELIX 25 25 THR B 56 SER B 63 1 8 HELIX 26 26 GLY B 77 LYS B 88 1 12 HELIX 27 27 PRO B 89 LEU B 91 5 3 HELIX 28 28 PHE B 104 GLU B 118 1 15 HELIX 29 29 GLY B 129 GLY B 137 1 9 HELIX 30 30 GLN B 145 ALA B 160 1 16 HELIX 31 31 GLY B 177 ASN B 209 1 33 HELIX 32 32 THR B 211 ASN B 224 1 14 HELIX 33 33 SER B 229 PHE B 239 1 11 HELIX 34 34 TYR B 248 ILE B 253 1 6 HELIX 35 35 GLY B 261 GLY B 274 1 14 HELIX 36 36 LEU B 277 SER B 291 1 15 HELIX 37 37 LEU B 292 LYS B 301 1 10 HELIX 38 38 ASP B 313 ASN B 348 1 36 HELIX 39 39 ASN B 352 PHE B 360 1 9 HELIX 40 40 GLN B 369 ASN B 381 1 13 HELIX 41 41 ASN B 386 LEU B 389 5 4 HELIX 42 42 ALA B 390 GLY B 415 1 26 HELIX 43 43 VAL B 418 ARG B 432 1 15 HELIX 44 44 PRO B 437 ALA B 450 1 14 SHEET 1 A 7 LEU A 51 PRO A 53 0 SHEET 2 A 7 VAL A 29 PHE A 32 1 N VAL A 29 O VAL A 52 SHEET 3 A 7 GLY A 7 VAL A 9 1 N VAL A 8 O SER A 30 SHEET 4 A 7 ARG A 69 LEU A 72 1 O LEU A 71 N VAL A 9 SHEET 5 A 7 ILE A 96 ASP A 99 1 O ILE A 98 N LEU A 72 SHEET 6 A 7 ASN A 121 SER A 128 1 O THR A 125 N ASP A 99 SHEET 7 A 7 SER A 139 GLY A 143 -1 O SER A 139 N SER A 128 SHEET 1 B 2 TYR A 453 LYS A 454 0 SHEET 2 B 2 VAL A 461 PHE A 462 -1 O PHE A 462 N TYR A 453 SHEET 1 C 7 LEU B 51 PRO B 53 0 SHEET 2 C 7 VAL B 29 PHE B 32 1 N VAL B 29 O VAL B 52 SHEET 3 C 7 ILE B 6 VAL B 9 1 N VAL B 8 O SER B 30 SHEET 4 C 7 ARG B 69 LEU B 72 1 O LEU B 71 N GLY B 7 SHEET 5 C 7 ILE B 96 ASP B 99 1 O ILE B 98 N LEU B 72 SHEET 6 C 7 ASN B 121 SER B 128 1 O THR B 125 N ASP B 99 SHEET 7 C 7 SER B 139 GLY B 144 -1 O SER B 139 N SER B 128 SHEET 1 D 2 TYR B 453 LYS B 454 0 SHEET 2 D 2 VAL B 461 PHE B 462 -1 O PHE B 462 N TYR B 453 CISPEP 1 THR A 66 PRO A 67 0 -0.41 CISPEP 2 THR B 66 PRO B 67 0 -0.48 SITE 1 AC1 20 ASN A 102 SER A 128 GLY A 129 GLY A 130 SITE 2 AC1 20 LYS A 183 HIS A 186 ASN A 187 GLU A 190 SITE 3 AC1 20 TYR A 191 ASN A 259 LYS A 260 ARG A 287 SITE 4 AC1 20 ILE A 365 HOH A 656 HOH A 657 HOH A 714 SITE 5 AC1 20 HOH A 946 ARG B 445 PHE B 448 HIS B 451 SITE 1 AC2 20 ARG A 445 PHE A 448 HIS A 451 ASN B 102 SITE 2 AC2 20 SER B 128 GLY B 129 GLY B 130 LYS B 183 SITE 3 AC2 20 HIS B 186 ASN B 187 GLU B 190 TYR B 191 SITE 4 AC2 20 LYS B 260 ARG B 287 ILE B 365 HOH B 661 SITE 5 AC2 20 HOH B 839 HOH B 915 HOH B 928 HOH B1264 CRYST1 68.004 108.718 133.505 90.00 90.00 90.00 P 21 21 21 8 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 0.014705 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007490 0.00000