HEADER TRANSFERASE 15-JUN-12 4AXX TITLE THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN TITLE 2 PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP 3-PHOSPHOGLYCERATE AND TITLE 3 BERYLLIUM TRIFLUORIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOGLYCERATE KINASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL MIGRATION-INDUCING GENE 10 PROTEIN, PRIMER RECOGNITION COMPND 5 PROTEIN 2, PRP 2; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET30A KEYWDS GROUND STATE ANALOGUE, HEREDITARY HEMOLYTIC ANEMIA, PHOSPHOPROTEIN, KEYWDS 2 GLYCOLYSIS, TRANSFERASE, PHOSPHORYL TRANSFER, NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.W.BOWLER REVDAT 3 20-DEC-23 4AXX 1 REMARK LINK REVDAT 2 02-OCT-13 4AXX 1 SEQADV SEQRES ATOM ANISOU REVDAT 1 26-JUN-13 4AXX 0 JRNL AUTH M.W.BOWLER,M.J.CLIFF,G.M.BLACKBURN,J.P.WALTHO JRNL TITL CATALYTIC ACTIVITY IN THE TRANSITIONS STATE ANALOGUE JRNL TITL 2 STABILISED CONFORMATION OF A PHOSPHORYL TRANSFER ENZYME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0116 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 32916 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1730 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) : 1.74 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2321 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 107 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3055 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 423 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.59000 REMARK 3 B22 (A**2) : 0.73000 REMARK 3 B33 (A**2) : -1.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.824 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3157 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2137 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4255 ; 1.544 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5274 ; 0.907 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 407 ; 6.576 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;43.146 ;25.678 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 570 ;14.039 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;16.544 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 487 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3457 ; 0.006 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 10 A 180 REMARK 3 RESIDUE RANGE : A 200 A 400 REMARK 3 ORIGIN FOR THE GROUP (A): -3.1077 8.4570 -20.0872 REMARK 3 T TENSOR REMARK 3 T11: 0.0185 T22: 0.0332 REMARK 3 T33: 0.0252 T12: 0.0078 REMARK 3 T13: 0.0116 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 0.8457 L22: 1.2039 REMARK 3 L33: 2.0865 L12: -0.5737 REMARK 3 L13: 0.7548 L23: -0.7879 REMARK 3 S TENSOR REMARK 3 S11: -0.0503 S12: -0.1103 S13: 0.0460 REMARK 3 S21: 0.1298 S22: 0.0528 S23: 0.0493 REMARK 3 S31: -0.1418 S32: -0.2212 S33: -0.0026 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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. DENSITY CLEAR FOR BEF3 ASSOCIATED WITH 3PG BUT AFTER REMARK 3 REFINEMENT A SMALL PEAK IS VISIBLE THAT MAY BE A BEF3 ASSOCIATED REMARK 3 WITH ADP (THE OTHER SIDE OF THE REACTION COORDINATE). REMARK 4 REMARK 4 4AXX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1290052913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 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 : C001 REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34680 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 29.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: PDB ENTRY 2WZC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 0.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32% PEG2000MME, 0.1M BIS/TRIS PH 6.5 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 19.41000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.27000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.27000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.41000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.40000 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: 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 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 1 REMARK 465 SER A 2 REMARK 465 LYS A 133 REMARK 465 ASP A 134 REMARK 465 ALA A 135 REMARK 465 SER A 136 REMARK 465 GLY A 137 REMARK 465 ASN A 138 REMARK 465 LYS A 139 REMARK 465 VAL A 140 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 N LYS A 141 O HOH A 2176 2.04 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 110 65.52 -155.29 REMARK 500 ASN A 121 112.61 -37.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 100 GLY A 101 -34.42 REMARK 500 GLU A 129 GLY A 130 -40.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2166 DISTANCE = 7.25 ANGSTROMS REMARK 525 HOH A2301 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A2421 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH A2422 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A2423 DISTANCE = 6.51 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1418 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 375 OD2 REMARK 620 2 ADP A1420 O2A 101.3 REMARK 620 3 ADP A1420 O3B 90.4 116.8 REMARK 620 4 ADP A1420 PB 106.2 86.3 31.9 REMARK 620 5 HOH A2236 O 84.6 83.4 159.8 166.4 REMARK 620 6 HOH A2388 O 86.9 157.3 83.9 111.9 76.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BEF A1422 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 3PG A1421 O2 REMARK 620 2 BEF A1422 F1 110.8 REMARK 620 3 BEF A1422 F2 100.0 113.4 REMARK 620 4 BEF A1422 F3 101.7 116.1 112.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PG A 1421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEF A 1422 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WZB RELATED DB: PDB REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN REMARK 900 PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP, 3PG AND MAGNESIUM REMARK 900 TRIFLUORIDE REMARK 900 RELATED ID: 2WZC RELATED DB: PDB REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN REMARK 900 PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP, 3PG AND ALUMINIUM REMARK 900 TETRAFLUORIDE REMARK 900 RELATED ID: 2WZD RELATED DB: PDB REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN REMARK 900 PHOSPHOGLYCERATE KINASE K219A MUTANT IN COMPLEX WITH ADP, 3PG AND REMARK 900 ALUMINIUM TRIFLUORIDE REMARK 900 RELATED ID: 2X13 RELATED DB: PDB REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN REMARK 900 PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP AND 3PHOSPHOGLYCERATE REMARK 900 RELATED ID: 2X14 RELATED DB: PDB REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN REMARK 900 PHOSPHOGLYCERATE KINASE K219A MUTANT IN COMPLEX WITH AMP-PCP AND 3PG REMARK 900 RELATED ID: 2X15 RELATED DB: PDB REMARK 900 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN REMARK 900 PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP AND 1,3- REMARK 900 BISPHOSPHOGLYCERATE REMARK 900 RELATED ID: 2XE6 RELATED DB: PDB REMARK 900 THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE REMARK 900 OPEN BINARY COMPLEX WITH 3PG REMARK 900 RELATED ID: 2XE7 RELATED DB: PDB REMARK 900 THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE REMARK 900 OPEN TERNARY COMPLEX WITH 3PG AND ADP REMARK 900 RELATED ID: 2XE8 RELATED DB: PDB REMARK 900 THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE REMARK 900 OPEN TERNARY COMPLEX WITH 3PG AND AMP- PNP REMARK 900 RELATED ID: 2Y3I RELATED DB: PDB REMARK 900 THE STRUCTURE OF THE FULLY CLOSED CONFORMATION OF HUMAN PGK IN REMARK 900 COMPLEX WITH L-ADP, 3PG AND THE TSA ALUMINIUM TETRAFLUORIDE REMARK 900 RELATED ID: 2YBE RELATED DB: PDB REMARK 900 THE STRUCTURE OF THE FULLY CLOSED CONFORMATION OF HUMAN PGK IN REMARK 900 COMPLEX WITH L-ADP, 3PG AND THE TSA ALUMINIUM TETRAFLUORIDE AT 2.0 REMARK 900 A RESOLUTION DBREF 4AXX A 1 417 UNP P00558 PGK1_HUMAN 1 417 SEQADV 4AXX ALA A 132 UNP P00558 GLY 132 CONFLICT SEQRES 1 A 417 MET SER LEU SER ASN LYS LEU THR LEU ASP LYS LEU ASP SEQRES 2 A 417 VAL LYS GLY LYS ARG VAL VAL MET ARG VAL ASP PHE ASN SEQRES 3 A 417 VAL PRO MET LYS ASN ASN GLN ILE THR ASN ASN GLN ARG SEQRES 4 A 417 ILE LYS ALA ALA VAL PRO SER ILE LYS PHE CYS LEU ASP SEQRES 5 A 417 ASN GLY ALA LYS SER VAL VAL LEU MET SER HIS LEU GLY SEQRES 6 A 417 ARG PRO ASP GLY VAL PRO MET PRO ASP LYS TYR SER LEU SEQRES 7 A 417 GLU PRO VAL ALA VAL GLU LEU LYS SER LEU LEU GLY LYS SEQRES 8 A 417 ASP VAL LEU PHE LEU LYS ASP CYS VAL GLY PRO GLU VAL SEQRES 9 A 417 GLU LYS ALA CYS ALA ASN PRO ALA ALA GLY SER VAL ILE SEQRES 10 A 417 LEU LEU GLU ASN LEU ARG PHE HIS VAL GLU GLU GLU GLY SEQRES 11 A 417 LYS ALA LYS ASP ALA SER GLY ASN LYS VAL LYS ALA GLU SEQRES 12 A 417 PRO ALA LYS ILE GLU ALA PHE ARG ALA SER LEU SER LYS SEQRES 13 A 417 LEU GLY ASP VAL TYR VAL ASN ASP ALA PHE GLY THR ALA SEQRES 14 A 417 HIS ARG ALA HIS SER SER MET VAL GLY VAL ASN LEU PRO SEQRES 15 A 417 GLN LYS ALA GLY GLY PHE LEU MET LYS LYS GLU LEU ASN SEQRES 16 A 417 TYR PHE ALA LYS ALA LEU GLU SER PRO GLU ARG PRO PHE SEQRES 17 A 417 LEU ALA ILE LEU GLY GLY ALA LYS VAL ALA ASP LYS ILE SEQRES 18 A 417 GLN LEU ILE ASN ASN MET LEU ASP LYS VAL ASN GLU MET SEQRES 19 A 417 ILE ILE GLY GLY GLY MET ALA PHE THR PHE LEU LYS VAL SEQRES 20 A 417 LEU ASN ASN MET GLU ILE GLY THR SER LEU PHE ASP GLU SEQRES 21 A 417 GLU GLY ALA LYS ILE VAL LYS ASP LEU MET SER LYS ALA SEQRES 22 A 417 GLU LYS ASN GLY VAL LYS ILE THR LEU PRO VAL ASP PHE SEQRES 23 A 417 VAL THR ALA ASP LYS PHE ASP GLU ASN ALA LYS THR GLY SEQRES 24 A 417 GLN ALA THR VAL ALA SER GLY ILE PRO ALA GLY TRP MET SEQRES 25 A 417 GLY LEU ASP CYS GLY PRO GLU SER SER LYS LYS TYR ALA SEQRES 26 A 417 GLU ALA VAL THR ARG ALA LYS GLN ILE VAL TRP ASN GLY SEQRES 27 A 417 PRO VAL GLY VAL PHE GLU TRP GLU ALA PHE ALA ARG GLY SEQRES 28 A 417 THR LYS ALA LEU MET ASP GLU VAL VAL LYS ALA THR SER SEQRES 29 A 417 ARG GLY CYS ILE THR ILE ILE GLY GLY GLY ASP THR ALA SEQRES 30 A 417 THR CYS CYS ALA LYS TRP ASN THR GLU ASP LYS VAL SER SEQRES 31 A 417 HIS VAL SER THR GLY GLY GLY ALA SER LEU GLU LEU LEU SEQRES 32 A 417 GLU GLY LYS VAL LEU PRO GLY VAL ASP ALA LEU SER ASN SEQRES 33 A 417 ILE HET MG A1418 1 HET CL A1419 1 HET ADP A1420 27 HET 3PG A1421 11 HET BEF A1422 4 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM 3PG 3-PHOSPHOGLYCERIC ACID HETNAM BEF BERYLLIUM TRIFLUORIDE ION FORMUL 2 MG MG 2+ FORMUL 3 CL CL 1- FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 3PG C3 H7 O7 P FORMUL 6 BEF BE F3 1- FORMUL 7 HOH *423(H2 O) HELIX 1 1 LEU A 9 LEU A 12 5 4 HELIX 2 2 ASN A 37 ASN A 53 1 17 HELIX 3 3 MET A 72 SER A 77 1 6 HELIX 4 4 LEU A 78 GLY A 90 1 13 HELIX 5 5 GLY A 101 ASN A 110 1 10 HELIX 6 6 ASN A 121 HIS A 125 5 5 HELIX 7 7 GLU A 143 LEU A 157 1 15 HELIX 8 8 ALA A 165 ALA A 169 5 5 HELIX 9 9 HIS A 173 GLY A 178 1 6 HELIX 10 10 GLY A 187 SER A 203 1 17 HELIX 11 11 LYS A 216 ILE A 221 1 6 HELIX 12 12 LEU A 223 LEU A 228 1 6 HELIX 13 13 MET A 240 ASN A 250 1 11 HELIX 14 14 ASP A 259 LYS A 264 1 6 HELIX 15 15 ILE A 265 ASN A 276 1 12 HELIX 16 16 GLY A 317 ALA A 331 1 15 HELIX 17 17 TRP A 345 PHE A 348 5 4 HELIX 18 18 ALA A 349 ARG A 365 1 17 HELIX 19 19 ASP A 375 TRP A 383 1 9 HELIX 20 20 GLY A 396 GLY A 405 1 10 HELIX 21 21 LEU A 408 ALA A 413 1 6 SHEET 1 AA 6 LEU A 94 PHE A 95 0 SHEET 2 AA 6 SER A 115 LEU A 118 1 O VAL A 116 N LEU A 94 SHEET 3 AA 6 SER A 57 MET A 61 1 O VAL A 58 N ILE A 117 SHEET 4 AA 6 ARG A 18 ARG A 22 1 O VAL A 19 N VAL A 59 SHEET 5 AA 6 VAL A 160 ASN A 163 1 O VAL A 160 N VAL A 20 SHEET 6 AA 6 LYS A 184 GLY A 186 1 O ALA A 185 N ASN A 163 SHEET 1 AB 2 MET A 29 LYS A 30 0 SHEET 2 AB 2 GLN A 33 ILE A 34 -1 O GLN A 33 N LYS A 30 SHEET 1 AC 6 LYS A 279 THR A 281 0 SHEET 2 AC 6 GLU A 233 ILE A 236 1 O MET A 234 N THR A 281 SHEET 3 AC 6 PHE A 208 LEU A 212 1 O ALA A 210 N ILE A 235 SHEET 4 AC 6 GLN A 333 ASN A 337 1 O GLN A 333 N LEU A 209 SHEET 5 AC 6 ILE A 368 GLY A 372 1 O ILE A 368 N ILE A 334 SHEET 6 AC 6 HIS A 391 SER A 393 1 O HIS A 391 N ILE A 371 SHEET 1 AD 3 THR A 298 THR A 302 0 SHEET 2 AD 3 ASP A 285 ALA A 289 -1 O PHE A 286 N ALA A 301 SHEET 3 AD 3 MET A 312 CYS A 316 -1 O MET A 312 N ALA A 289 LINK OD2 ASP A 375 MG MG A1418 1555 1555 1.97 LINK MG MG A1418 O2A ADP A1420 1555 1555 1.91 LINK MG MG A1418 O3B ADP A1420 1555 1555 1.80 LINK MG MG A1418 PB ADP A1420 1555 1555 2.65 LINK MG MG A1418 O HOH A2236 1555 1555 2.42 LINK MG MG A1418 O HOH A2388 1555 1555 2.32 LINK O2 3PG A1421 BE BEF A1422 1555 1555 1.73 CISPEP 1 ARG A 206 PRO A 207 0 4.49 SITE 1 AC1 5 ASP A 375 ADP A1420 BEF A1422 HOH A2236 SITE 2 AC1 5 HOH A2388 SITE 1 AC2 3 ARG A 66 LYS A 216 ASP A 219 SITE 1 AC3 29 GLY A 214 ALA A 215 LYS A 216 LYS A 220 SITE 2 AC3 29 GLY A 238 GLY A 239 PHE A 242 LEU A 257 SITE 3 AC3 29 GLY A 313 LEU A 314 ASN A 337 PRO A 339 SITE 4 AC3 29 GLY A 341 VAL A 342 GLU A 344 GLY A 373 SITE 5 AC3 29 GLY A 374 ASP A 375 THR A 376 MG A1418 SITE 6 AC3 29 BEF A1422 HOH A2235 HOH A2236 HOH A2286 SITE 7 AC3 29 HOH A2340 HOH A2386 HOH A2388 HOH A2418 SITE 8 AC3 29 HOH A2419 SITE 1 AC4 16 ASP A 24 ASN A 26 ARG A 39 HIS A 63 SITE 2 AC4 16 ARG A 66 ARG A 123 GLY A 167 THR A 168 SITE 3 AC4 16 ARG A 171 LYS A 216 BEF A1422 HOH A2051 SITE 4 AC4 16 HOH A2167 HOH A2193 HOH A2196 HOH A2388 SITE 1 AC5 13 ARG A 39 LYS A 216 LYS A 220 GLY A 373 SITE 2 AC5 13 GLY A 374 GLY A 396 GLY A 397 MG A1418 SITE 3 AC5 13 ADP A1420 3PG A1421 HOH A2196 HOH A2236 SITE 4 AC5 13 HOH A2388 CRYST1 38.820 90.800 108.540 90.00 90.00 90.00 P 21 21 21 4 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 0.025760 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009213 0.00000