PDB Short entry for 3C39 HEADER TRANSFERASE 28-JAN-08 3C39 TITLE CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLYCERATE KINASE BOUND TO 3- TITLE 2 PHOSPHOGLYCERATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOGLYCERATE KINASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3-PHOSPHOGLYCERATE KINASE, PRIMER RECOGNITION PROTEIN 2, PRP COMPND 5 2, CELL MIGRATION-INDUCING GENE 10 PROTEIN; COMPND 6 EC: 2.7.2.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PGK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3)/PDIA17; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TWO DOMAIN, KINASE, BETA SANDWICH, ACETYLATION, ATP-BINDING, KEYWDS 2 CYTOPLASM, DISEASE MUTATION, GLYCOLYSIS, HEREDITARY HEMOLYTIC KEYWDS 3 ANEMIA, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, POLYMORPHISM, KEYWDS 4 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.T.AROLD,C.GONDEAU,C.LIONNE,L.CHALOIN REVDAT 3 01-NOV-23 3C39 1 REMARK SEQADV REVDAT 2 24-FEB-09 3C39 1 VERSN REVDAT 1 01-JUL-08 3C39 0 JRNL AUTH C.GONDEAU,L.CHALOIN,P.LALLEMAND,B.ROY,C.PERIGAUD,T.BARMAN, JRNL AUTH 2 A.VARGA,M.VAS,C.LIONNE,S.T.AROLD JRNL TITL MOLECULAR BASIS FOR THE LACK OF ENANTIOSELECTIVITY OF HUMAN JRNL TITL 2 3-PHOSPHOGLYCERATE KINASE JRNL REF NUCLEIC ACIDS RES. V. 36 3620 2008 JRNL REFN ISSN 0305-1048 JRNL PMID 18463139 JRNL DOI 10.1093/NAR/GKN212 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0062 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 77.1 REMARK 3 NUMBER OF REFLECTIONS : 44499 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 + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1435 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1975 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 45.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5949 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 495 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.88000 REMARK 3 B22 (A**2) : -1.27000 REMARK 3 B33 (A**2) : 1.87000 REMARK 3 B12 (A**2) : 0.01000 REMARK 3 B13 (A**2) : -0.35000 REMARK 3 B23 (A**2) : 0.91000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.230 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.212 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.223 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6059 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8155 ; 1.905 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 786 ; 6.886 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 227 ;42.373 ;25.595 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1123 ;16.830 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.414 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 935 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4398 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3911 ; 1.090 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6253 ; 1.831 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2148 ; 2.991 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1902 ; 4.605 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3C39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046285. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN COOLED CHANNEL REMARK 200 -CUT SILICON MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44499 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 91.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 77.1 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1VJC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.6M NAKPO4, PH 8.3, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 ASP A 133 REMARK 465 ALA A 134 REMARK 465 SER A 135 REMARK 465 GLY A 136 REMARK 465 ASN A 137 REMARK 465 LYS A 138 REMARK 465 VAL A 139 REMARK 465 GLY A 373 REMARK 465 ASP A 374 REMARK 465 THR A 375 REMARK 465 ALA A 376 REMARK 465 THR A 377 REMARK 465 CYS A 378 REMARK 465 CYS A 379 REMARK 465 ALA A 380 REMARK 465 LYS A 381 REMARK 465 TRP A 382 REMARK 465 ASN A 383 REMARK 465 THR A 384 REMARK 465 GLU A 385 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 HIS B -1 REMARK 465 MET B 0 REMARK 465 SER B 1 REMARK 465 CYS B 98 REMARK 465 VAL B 99 REMARK 465 GLY B 100 REMARK 465 PRO B 101 REMARK 465 GLU B 102 REMARK 465 VAL B 103 REMARK 465 GLY B 373 REMARK 465 ASP B 374 REMARK 465 THR B 375 REMARK 465 ALA B 376 REMARK 465 THR B 377 REMARK 465 CYS B 378 REMARK 465 CYS B 379 REMARK 465 ALA B 380 REMARK 465 LYS B 381 REMARK 465 TRP B 382 REMARK 465 ASN B 383 REMARK 465 THR B 384 REMARK 465 GLU B 385 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 B 771 O HOH B 779 2.05 REMARK 500 OD2 ASP A 91 O HOH A 496 2.12 REMARK 500 O HOH A 629 O HOH A 647 2.17 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 OD1 ASP A 386 O HOH B 790 1655 1.98 REMARK 500 O LEU A 247 O HOH B 706 1546 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 VAL A 327 CB VAL A 327 CG1 0.137 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 LYS A 96 CD - CE - NZ ANGL. DEV. = -20.1 DEGREES REMARK 500 ARG A 329 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 LEU B 2 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 LYS B 191 CD - CE - NZ ANGL. DEV. = 19.1 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 ASN A 109 63.17 -157.02 REMARK 500 ASN A 120 119.13 -39.21 REMARK 500 ASN B 30 -137.16 77.23 REMARK 500 LYS B 96 2.30 -63.09 REMARK 500 ASN B 109 76.60 -175.76 REMARK 500 ARG B 122 4.07 -69.11 REMARK 500 ASN B 294 53.65 -96.23 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 3PG B 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PG A 417 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZGV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLYCERATE KINASE BOUND TO D-ADP REMARK 900 RELATED ID: 3C3A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLYCERATE KINASE BOUND TO 3- REMARK 900 PHOSPHOGLYCERATE AND L-ADP REMARK 900 RELATED ID: 3C3B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLYCERATE KINASE BOUND TO D-CDP REMARK 900 RELATED ID: 3C3C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLYCERATE KINASE BOUND TO 3- REMARK 900 PHOSPHOGLYCERATE AND L-CDP DBREF 3C39 A 0 416 UNP P00558 PGK1_HUMAN 1 417 DBREF 3C39 B 0 416 UNP P00558 PGK1_HUMAN 1 417 SEQADV 3C39 GLY A -3 UNP P00558 EXPRESSION TAG SEQADV 3C39 SER A -2 UNP P00558 EXPRESSION TAG SEQADV 3C39 HIS A -1 UNP P00558 EXPRESSION TAG SEQADV 3C39 GLY B -3 UNP P00558 EXPRESSION TAG SEQADV 3C39 SER B -2 UNP P00558 EXPRESSION TAG SEQADV 3C39 HIS B -1 UNP P00558 EXPRESSION TAG SEQRES 1 A 420 GLY SER HIS MET SER LEU SER ASN LYS LEU THR LEU ASP SEQRES 2 A 420 LYS LEU ASP VAL LYS GLY LYS ARG VAL VAL MET ARG VAL SEQRES 3 A 420 ASP PHE ASN VAL PRO MET LYS ASN ASN GLN ILE THR ASN SEQRES 4 A 420 ASN GLN ARG ILE LYS ALA ALA VAL PRO SER ILE LYS PHE SEQRES 5 A 420 CYS LEU ASP ASN GLY ALA LYS SER VAL VAL LEU MET SER SEQRES 6 A 420 HIS LEU GLY ARG PRO ASP GLY VAL PRO MET PRO ASP LYS SEQRES 7 A 420 TYR SER LEU GLU PRO VAL ALA VAL GLU LEU LYS SER LEU SEQRES 8 A 420 LEU GLY LYS ASP VAL LEU PHE LEU LYS ASP CYS VAL GLY SEQRES 9 A 420 PRO GLU VAL GLU LYS ALA CYS ALA ASN PRO ALA ALA GLY SEQRES 10 A 420 SER VAL ILE LEU LEU GLU ASN LEU ARG PHE HIS VAL GLU SEQRES 11 A 420 GLU GLU GLY LYS GLY LYS ASP ALA SER GLY ASN LYS VAL SEQRES 12 A 420 LYS ALA GLU PRO ALA LYS ILE GLU ALA PHE ARG ALA SER SEQRES 13 A 420 LEU SER LYS LEU GLY ASP VAL TYR VAL ASN ASP ALA PHE SEQRES 14 A 420 GLY THR ALA HIS ARG ALA HIS SER SER MET VAL GLY VAL SEQRES 15 A 420 ASN LEU PRO GLN LYS ALA GLY GLY PHE LEU MET LYS LYS SEQRES 16 A 420 GLU LEU ASN TYR PHE ALA LYS ALA LEU GLU SER PRO GLU SEQRES 17 A 420 ARG PRO PHE LEU ALA ILE LEU GLY GLY ALA LYS VAL ALA SEQRES 18 A 420 ASP LYS ILE GLN LEU ILE ASN ASN MET LEU ASP LYS VAL SEQRES 19 A 420 ASN GLU MET ILE ILE GLY GLY GLY MET ALA PHE THR PHE SEQRES 20 A 420 LEU LYS VAL LEU ASN ASN MET GLU ILE GLY THR SER LEU SEQRES 21 A 420 PHE ASP GLU GLU GLY ALA LYS ILE VAL LYS ASP LEU MET SEQRES 22 A 420 SER LYS ALA GLU LYS ASN GLY VAL LYS ILE THR LEU PRO SEQRES 23 A 420 VAL ASP PHE VAL THR ALA ASP LYS PHE ASP GLU ASN ALA SEQRES 24 A 420 LYS THR GLY GLN ALA THR VAL ALA SER GLY ILE PRO ALA SEQRES 25 A 420 GLY TRP MET GLY LEU ASP CYS GLY PRO GLU SER SER LYS SEQRES 26 A 420 LYS TYR ALA GLU ALA VAL THR ARG ALA LYS GLN ILE VAL SEQRES 27 A 420 TRP ASN GLY PRO VAL GLY VAL PHE GLU TRP GLU ALA PHE SEQRES 28 A 420 ALA ARG GLY THR LYS ALA LEU MET ASP GLU VAL VAL LYS SEQRES 29 A 420 ALA THR SER ARG GLY CYS ILE THR ILE ILE GLY GLY GLY SEQRES 30 A 420 ASP THR ALA THR CYS CYS ALA LYS TRP ASN THR GLU ASP SEQRES 31 A 420 LYS VAL SER HIS VAL SER THR GLY GLY GLY ALA SER LEU SEQRES 32 A 420 GLU LEU LEU GLU GLY LYS VAL LEU PRO GLY VAL ASP ALA SEQRES 33 A 420 LEU SER ASN ILE SEQRES 1 B 420 GLY SER HIS MET SER LEU SER ASN LYS LEU THR LEU ASP SEQRES 2 B 420 LYS LEU ASP VAL LYS GLY LYS ARG VAL VAL MET ARG VAL SEQRES 3 B 420 ASP PHE ASN VAL PRO MET LYS ASN ASN GLN ILE THR ASN SEQRES 4 B 420 ASN GLN ARG ILE LYS ALA ALA VAL PRO SER ILE LYS PHE SEQRES 5 B 420 CYS LEU ASP ASN GLY ALA LYS SER VAL VAL LEU MET SER SEQRES 6 B 420 HIS LEU GLY ARG PRO ASP GLY VAL PRO MET PRO ASP LYS SEQRES 7 B 420 TYR SER LEU GLU PRO VAL ALA VAL GLU LEU LYS SER LEU SEQRES 8 B 420 LEU GLY LYS ASP VAL LEU PHE LEU LYS ASP CYS VAL GLY SEQRES 9 B 420 PRO GLU VAL GLU LYS ALA CYS ALA ASN PRO ALA ALA GLY SEQRES 10 B 420 SER VAL ILE LEU LEU GLU ASN LEU ARG PHE HIS VAL GLU SEQRES 11 B 420 GLU GLU GLY LYS GLY LYS ASP ALA SER GLY ASN LYS VAL SEQRES 12 B 420 LYS ALA GLU PRO ALA LYS ILE GLU ALA PHE ARG ALA SER SEQRES 13 B 420 LEU SER LYS LEU GLY ASP VAL TYR VAL ASN ASP ALA PHE SEQRES 14 B 420 GLY THR ALA HIS ARG ALA HIS SER SER MET VAL GLY VAL SEQRES 15 B 420 ASN LEU PRO GLN LYS ALA GLY GLY PHE LEU MET LYS LYS SEQRES 16 B 420 GLU LEU ASN TYR PHE ALA LYS ALA LEU GLU SER PRO GLU SEQRES 17 B 420 ARG PRO PHE LEU ALA ILE LEU GLY GLY ALA LYS VAL ALA SEQRES 18 B 420 ASP LYS ILE GLN LEU ILE ASN ASN MET LEU ASP LYS VAL SEQRES 19 B 420 ASN GLU MET ILE ILE GLY GLY GLY MET ALA PHE THR PHE SEQRES 20 B 420 LEU LYS VAL LEU ASN ASN MET GLU ILE GLY THR SER LEU SEQRES 21 B 420 PHE ASP GLU GLU GLY ALA LYS ILE VAL LYS ASP LEU MET SEQRES 22 B 420 SER LYS ALA GLU LYS ASN GLY VAL LYS ILE THR LEU PRO SEQRES 23 B 420 VAL ASP PHE VAL THR ALA ASP LYS PHE ASP GLU ASN ALA SEQRES 24 B 420 LYS THR GLY GLN ALA THR VAL ALA SER GLY ILE PRO ALA SEQRES 25 B 420 GLY TRP MET GLY LEU ASP CYS GLY PRO GLU SER SER LYS SEQRES 26 B 420 LYS TYR ALA GLU ALA VAL THR ARG ALA LYS GLN ILE VAL SEQRES 27 B 420 TRP ASN GLY PRO VAL GLY VAL PHE GLU TRP GLU ALA PHE SEQRES 28 B 420 ALA ARG GLY THR LYS ALA LEU MET ASP GLU VAL VAL LYS SEQRES 29 B 420 ALA THR SER ARG GLY CYS ILE THR ILE ILE GLY GLY GLY SEQRES 30 B 420 ASP THR ALA THR CYS CYS ALA LYS TRP ASN THR GLU ASP SEQRES 31 B 420 LYS VAL SER HIS VAL SER THR GLY GLY GLY ALA SER LEU SEQRES 32 B 420 GLU LEU LEU GLU GLY LYS VAL LEU PRO GLY VAL ASP ALA SEQRES 33 B 420 LEU SER ASN ILE HET 3PG A 417 11 HET 3PG B 417 11 HETNAM 3PG 3-PHOSPHOGLYCERIC ACID FORMUL 3 3PG 2(C3 H7 O7 P) FORMUL 5 HOH *495(H2 O) HELIX 1 1 THR A 7 LEU A 11 5 5 HELIX 2 2 ASN A 36 ALA A 42 1 7 HELIX 3 3 ALA A 42 ASN A 52 1 11 HELIX 4 4 LEU A 77 GLY A 89 1 13 HELIX 5 5 GLY A 100 ASN A 109 1 10 HELIX 6 6 ASN A 120 HIS A 124 5 5 HELIX 7 7 GLU A 142 LEU A 156 1 15 HELIX 8 8 ALA A 164 ALA A 168 5 5 HELIX 9 9 HIS A 172 GLY A 177 1 6 HELIX 10 10 GLY A 186 SER A 202 1 17 HELIX 11 11 LYS A 219 ASP A 228 1 10 HELIX 12 12 GLY A 238 ASN A 249 1 12 HELIX 13 13 ASP A 258 LYS A 263 1 6 HELIX 14 14 ILE A 264 GLY A 276 1 13 HELIX 15 15 GLY A 316 ALA A 330 1 15 HELIX 16 16 TRP A 344 PHE A 347 5 4 HELIX 17 17 ALA A 348 ARG A 364 1 17 HELIX 18 18 GLY A 395 GLU A 403 1 9 HELIX 19 19 LEU A 407 ALA A 412 1 6 HELIX 20 20 THR B 7 LEU B 11 5 5 HELIX 21 21 ASN B 36 ALA B 41 1 6 HELIX 22 22 ALA B 42 ASN B 52 1 11 HELIX 23 23 LEU B 77 GLY B 89 1 13 HELIX 24 24 ASN B 120 PHE B 123 5 4 HELIX 25 25 HIS B 124 GLY B 129 1 6 HELIX 26 26 GLU B 142 LYS B 155 1 14 HELIX 27 27 ALA B 164 ALA B 168 5 5 HELIX 28 28 HIS B 172 GLY B 177 1 6 HELIX 29 29 GLY B 186 GLU B 201 1 16 HELIX 30 30 VAL B 216 ASP B 218 5 3 HELIX 31 31 LYS B 219 ASP B 228 1 10 HELIX 32 32 MET B 239 ASN B 248 1 10 HELIX 33 33 ASP B 258 LYS B 263 1 6 HELIX 34 34 ILE B 264 GLY B 276 1 13 HELIX 35 35 GLY B 316 ALA B 330 1 15 HELIX 36 36 TRP B 344 PHE B 347 5 4 HELIX 37 37 ALA B 348 ARG B 364 1 17 HELIX 38 38 GLY B 394 GLY B 404 1 11 HELIX 39 39 LEU B 407 ALA B 412 1 6 SHEET 1 A 6 LEU A 93 PHE A 94 0 SHEET 2 A 6 SER A 114 LEU A 117 1 O LEU A 117 N LEU A 93 SHEET 3 A 6 SER A 56 MET A 60 1 N LEU A 59 O ILE A 116 SHEET 4 A 6 ARG A 17 ARG A 21 1 N MET A 20 O VAL A 58 SHEET 5 A 6 VAL A 159 ASN A 162 1 O VAL A 161 N VAL A 19 SHEET 6 A 6 LYS A 183 GLY A 185 1 O ALA A 184 N ASN A 162 SHEET 1 B 2 MET A 28 LYS A 29 0 SHEET 2 B 2 GLN A 32 ILE A 33 -1 O GLN A 32 N LYS A 29 SHEET 1 C 6 LYS A 278 THR A 280 0 SHEET 2 C 6 GLU A 232 GLY A 236 1 N MET A 233 O THR A 280 SHEET 3 C 6 PHE A 207 GLY A 212 1 N LEU A 211 O ILE A 234 SHEET 4 C 6 GLN A 332 ASN A 336 1 O GLN A 332 N LEU A 208 SHEET 5 C 6 ILE A 367 ILE A 370 1 O ILE A 369 N ILE A 333 SHEET 6 C 6 HIS A 390 VAL A 391 1 O HIS A 390 N ILE A 370 SHEET 1 D 3 THR A 297 THR A 301 0 SHEET 2 D 3 ASP A 284 ALA A 288 -1 N PHE A 285 O ALA A 300 SHEET 3 D 3 MET A 311 CYS A 315 -1 O LEU A 313 N VAL A 286 SHEET 1 E 6 LEU B 93 LEU B 95 0 SHEET 2 E 6 SER B 114 LEU B 118 1 O VAL B 115 N LEU B 93 SHEET 3 E 6 SER B 56 MET B 60 1 N LEU B 59 O ILE B 116 SHEET 4 E 6 ARG B 17 ARG B 21 1 N VAL B 18 O SER B 56 SHEET 5 E 6 VAL B 159 ASN B 162 1 O VAL B 161 N VAL B 19 SHEET 6 E 6 LYS B 183 GLY B 185 1 O ALA B 184 N ASN B 162 SHEET 1 F 2 MET B 28 LYS B 29 0 SHEET 2 F 2 GLN B 32 ILE B 33 -1 O GLN B 32 N LYS B 29 SHEET 1 G 2 LYS B 130 LYS B 132 0 SHEET 2 G 2 LYS B 138 LYS B 140 -1 O VAL B 139 N GLY B 131 SHEET 1 H 6 LYS B 278 THR B 280 0 SHEET 2 H 6 GLU B 232 GLY B 236 1 N MET B 233 O THR B 280 SHEET 3 H 6 PHE B 207 GLY B 212 1 N LEU B 211 O ILE B 234 SHEET 4 H 6 GLN B 332 ASN B 336 1 O GLN B 332 N LEU B 208 SHEET 5 H 6 ILE B 367 ILE B 370 1 O ILE B 369 N TRP B 335 SHEET 6 H 6 HIS B 390 VAL B 391 1 O HIS B 390 N ILE B 370 SHEET 1 I 3 THR B 297 THR B 301 0 SHEET 2 I 3 ASP B 284 ALA B 288 -1 N PHE B 285 O ALA B 300 SHEET 3 I 3 MET B 311 CYS B 315 -1 O MET B 311 N ALA B 288 CISPEP 1 ARG A 205 PRO A 206 0 -1.97 CISPEP 2 ARG B 205 PRO B 206 0 -1.20 CISPEP 3 GLY B 371 GLY B 372 0 -2.14 SITE 1 AC1 8 ASP B 23 ASN B 25 ARG B 38 HIS B 62 SITE 2 AC1 8 ARG B 65 ARG B 122 GLY B 166 ARG B 170 SITE 1 AC2 8 ASP A 23 ASN A 25 ARG A 38 HIS A 62 SITE 2 AC2 8 ARG A 65 ARG A 122 GLY A 166 ARG A 170 CRYST1 35.616 55.790 93.230 79.18 84.33 83.23 P 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 0.028077 -0.003335 -0.002229 0.00000 SCALE2 0.000000 0.018050 -0.003269 0.00000 SCALE3 0.000000 0.000000 0.010954 0.00000