PDB Short entry for 2WZD HEADER TRANSFERASE 27-NOV-09 2WZD TITLE THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN TITLE 2 PHOSPHOGLYCERATE KINASE K219A MUTANT IN COMPLEX WITH ADP, 3PG AND TITLE 3 ALUMINIUM TRIFLUORIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOGLYCERATE KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-417; COMPND 5 SYNONYM: PRIMER RECOGNITION PROTEIN 2, PRP 2, CELL MIGRATION-INDUCING COMPND 6 GENE 10 PROTEIN; COMPND 7 EC: 2.7.2.3; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: COMPLEXED WITH ADP, 3PG AND ALUMINIUM TRIFLUORIDE 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 KEYWDS TRANSFERASE, HEREDITARY HEMOLYTIC ANEMIA, PHOSPHOPROTEIN, KINASE, KEYWDS 2 GLYCOLYSIS, NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.W.BOWLER,M.J.CLIFF,J.P.M.MARSTON,N.J.BAXTER,A.M.H.HOWNSLOW, AUTHOR 2 A.V.VARGA,J.SZABO,M.VAS,G.M.BLACKBURN,J.P.WALTHO REVDAT 5 20-DEC-23 2WZD 1 REMARK LINK REVDAT 4 07-DEC-11 2WZD 1 JRNL REVDAT 3 13-JUL-11 2WZD 1 VERSN REVDAT 2 28-APR-10 2WZD 1 JRNL REVDAT 1 14-APR-10 2WZD 0 JRNL AUTH M.J.CLIFF,M.W.BOWLER,J.SZABO,J.P.M.MARSTON,A.V.VARGA, JRNL AUTH 2 A.M.H.HOWNSLOW,N.J.BAXTER,G.M.BLACKBURN,M.VAS,J.P.WALTHO JRNL TITL TRANSITION STATE ANALOGUE STRUCTURES OF HUMAN JRNL TITL 2 PHOSPHOGLYCERATE KINASE ESTABLISH THE IMPORTANCE OF CHARGE JRNL TITL 3 BALANCE IN CATALYSIS. JRNL REF J.AM.CHEM.SOC. V. 132 6507 2010 JRNL REFN ISSN 0002-7863 JRNL PMID 20397725 JRNL DOI 10.1021/JA100974T REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 52652 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2800 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) : 1.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3608 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 177 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3036 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 466 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 14.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : 0.95000 REMARK 3 B33 (A**2) : -0.59000 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): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.787 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3161 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2141 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4276 ; 1.646 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5291 ; 0.942 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 415 ; 7.384 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;41.543 ;25.714 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 574 ;13.274 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;18.555 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 489 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3482 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 568 ; 0.001 ; 0.020 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): 2019 ; 0.811 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 837 ; 0.267 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3238 ; 1.352 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1142 ; 2.279 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1032 ; 3.644 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 189 REMARK 3 ORIGIN FOR THE GROUP (A): 3.4180 3.6669 -5.4552 REMARK 3 T TENSOR REMARK 3 T11: 0.1460 T22: 0.0764 REMARK 3 T33: 0.0102 T12: 0.0723 REMARK 3 T13: -0.0103 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 2.4460 L22: 4.2064 REMARK 3 L33: 2.4891 L12: -1.3957 REMARK 3 L13: 0.7457 L23: -0.9031 REMARK 3 S TENSOR REMARK 3 S11: -0.3254 S12: -0.3498 S13: 0.1334 REMARK 3 S21: 0.7102 S22: 0.3492 S23: -0.0421 REMARK 3 S31: -0.2366 S32: -0.1907 S33: -0.0238 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 190 A 416 REMARK 3 ORIGIN FOR THE GROUP (A): -5.6746 10.4044 -31.9151 REMARK 3 T TENSOR REMARK 3 T11: 0.0422 T22: 0.0528 REMARK 3 T33: 0.0248 T12: -0.0035 REMARK 3 T13: -0.0016 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 1.2674 L22: 1.7941 REMARK 3 L33: 1.1430 L12: -0.6381 REMARK 3 L13: 0.2897 L23: -0.6958 REMARK 3 S TENSOR REMARK 3 S11: 0.0577 S12: 0.0773 S13: -0.0025 REMARK 3 S21: -0.1597 S22: -0.0339 S23: 0.0824 REMARK 3 S31: 0.0364 S32: -0.0226 S33: -0.0238 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. THE METAL FLUORIDE IS MODELED AS AF33 WITH A REMARK 3 COORDINATING WATER MOLECULE (A3000)AS THIS IS THE OBSERVED REMARK 3 SPECIES IN 19F-NMR EXPERIEMNTS. REMARK 4 REMARK 4 2WZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1290041851. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-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 : C111 REMARK 200 OPTICS : GE211 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 : 55495 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3C39 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% 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 19.69000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.24000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.79500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.24000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.69000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.79500 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 220 TO ALA 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 0 REMARK 465 SER A 1 REMARK 465 LYS A 132 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 LYS A 140 REMARK 465 ALA A 141 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 CG1 VAL A 43 NZ LYS A 47 1.52 REMARK 500 NE2 GLN A 299 O HOH A 2365 1.57 REMARK 500 O HOH A 2040 O HOH A 2044 1.91 REMARK 500 NZ LYS A 10 O HOH A 2021 1.97 REMARK 500 OD1 ASP A 386 O HOH A 2430 2.04 REMARK 500 OD2 ASP A 67 O HOH A 2087 2.11 REMARK 500 OD1 ASP A 258 O HOH A 2303 2.12 REMARK 500 O LYS A 74 O HOH A 2103 2.15 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 ARG A 364 NE - CZ - NH1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 364 NE - CZ - NH2 ANGL. DEV. = -5.6 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 31 -2.57 74.52 REMARK 500 ASN A 120 110.78 -33.45 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 99 GLY A 100 69.40 REMARK 500 GLU A 128 GLY A 129 -52.56 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 A2082 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A2153 DISTANCE = 6.61 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 A1417 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 374 OD2 REMARK 620 2 AF3 A1419 F1 174.0 REMARK 620 3 ADP A1420 O1A 97.2 86.7 REMARK 620 4 ADP A1420 O1B 88.0 87.3 91.4 REMARK 620 5 HOH A2454 O 90.4 94.4 87.8 178.2 REMARK 620 6 HOH A2462 O 93.6 83.1 167.9 94.4 86.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AF3 A1419 AL REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A1420 O3B REMARK 620 2 AF3 A1419 F1 90.6 REMARK 620 3 AF3 A1419 F2 94.3 92.3 REMARK 620 4 AF3 A1419 F3 91.5 177.1 89.5 REMARK 620 5 ADP A1420 O1B 48.2 55.8 66.0 127.0 REMARK 620 6 3PG A1421 O1 142.4 64.9 60.9 114.1 94.5 REMARK 620 7 3PG A1421 O2 175.3 92.4 89.1 85.4 136.4 42.2 REMARK 620 8 HOH A3000 O 91.9 90.2 173.3 87.8 120.3 115.0 84.6 REMARK 620 N 1 2 3 4 5 6 7 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 1417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AF3 A 1419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PG A 1421 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 DBREF 2WZD A 0 416 UNP P00558 PGK1_HUMAN 1 417 SEQADV 2WZD ALA A 219 UNP P00558 LYS 220 ENGINEERED MUTATION 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 GLY 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 ALA 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 A1417 1 HET CL A1418 1 HET AF3 A1419 4 HET ADP A1420 27 HET 3PG A1421 11 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM AF3 ALUMINUM FLUORIDE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM 3PG 3-PHOSPHOGLYCERIC ACID FORMUL 2 MG MG 2+ FORMUL 3 CL CL 1- FORMUL 4 AF3 AL F3 FORMUL 5 ADP C10 H15 N5 O10 P2 FORMUL 6 3PG C3 H7 O7 P FORMUL 7 HOH *466(H2 O) HELIX 1 1 LEU A 8 LEU A 11 5 4 HELIX 2 2 ASN A 36 ASN A 52 1 17 HELIX 3 3 MET A 71 SER A 76 1 6 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 LYS A 155 1 14 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 215 GLN A 221 1 7 HELIX 12 12 LEU A 222 LEU A 227 1 6 HELIX 13 13 MET A 239 ASN A 249 1 11 HELIX 14 14 ASP A 258 LYS A 263 1 6 HELIX 15 15 ILE A 264 GLY A 276 1 13 HELIX 16 16 GLY A 316 ALA A 330 1 15 HELIX 17 17 TRP A 344 PHE A 347 5 4 HELIX 18 18 ALA A 348 ARG A 364 1 17 HELIX 19 19 ASP A 374 TRP A 382 1 9 HELIX 20 20 GLY A 395 GLU A 403 1 9 HELIX 21 21 LEU A 407 ALA A 412 1 6 SHEET 1 AA 6 LEU A 93 PHE A 94 0 SHEET 2 AA 6 SER A 114 LEU A 117 1 O VAL A 115 N LEU A 93 SHEET 3 AA 6 SER A 56 MET A 60 1 O VAL A 57 N ILE A 116 SHEET 4 AA 6 ARG A 17 ARG A 21 1 O VAL A 18 N VAL A 58 SHEET 5 AA 6 VAL A 159 ASN A 162 1 O VAL A 159 N VAL A 19 SHEET 6 AA 6 LYS A 183 GLY A 185 1 O ALA A 184 N ASN A 162 SHEET 1 AB 2 MET A 28 LYS A 29 0 SHEET 2 AB 2 GLN A 32 ILE A 33 -1 O GLN A 32 N LYS A 29 SHEET 1 AC 6 LYS A 278 THR A 280 0 SHEET 2 AC 6 GLU A 232 ILE A 235 1 O MET A 233 N THR A 280 SHEET 3 AC 6 PHE A 207 LEU A 211 1 O ALA A 209 N ILE A 234 SHEET 4 AC 6 GLN A 332 ASN A 336 1 O GLN A 332 N LEU A 208 SHEET 5 AC 6 ILE A 367 GLY A 371 1 O ILE A 367 N ILE A 333 SHEET 6 AC 6 HIS A 390 SER A 392 1 O HIS A 390 N ILE A 370 SHEET 1 AD 3 THR A 297 THR A 301 0 SHEET 2 AD 3 ASP A 284 ALA A 288 -1 O PHE A 285 N ALA A 300 SHEET 3 AD 3 MET A 311 CYS A 315 -1 O MET A 311 N ALA A 288 LINK OD2 ASP A 374 MG MG A1417 1555 1555 2.04 LINK MG MG A1417 F1 AF3 A1419 1555 1555 2.03 LINK MG MG A1417 O1A ADP A1420 1555 1555 2.06 LINK MG MG A1417 O1B ADP A1420 1555 1555 2.01 LINK MG MG A1417 O HOH A2454 1555 1555 2.09 LINK MG MG A1417 O HOH A2462 1555 1555 2.08 LINK AL AF3 A1419 O3B ADP A1420 1555 1555 1.92 LINK AL AF3 A1419 O1B ADP A1420 1555 1555 3.36 LINK AL AF3 A1419 O1 3PG A1421 1555 1555 3.26 LINK AL AF3 A1419 O2 3PG A1421 1555 1555 1.98 LINK AL AF3 A1419 O HOH A3000 1555 1555 1.92 CISPEP 1 ARG A 205 PRO A 206 0 5.70 SITE 1 AC1 5 ASP A 374 AF3 A1419 ADP A1420 HOH A2454 SITE 2 AC1 5 HOH A2462 SITE 1 AC2 4 ARG A 65 LYS A 215 ASP A 218 HOH A2254 SITE 1 AC3 13 ARG A 38 LYS A 215 GLY A 372 GLY A 373 SITE 2 AC3 13 GLY A 395 GLY A 396 MG A1417 ADP A1420 SITE 3 AC3 13 3PG A1421 HOH A2208 HOH A2454 HOH A2462 SITE 4 AC3 13 HOH A3000 SITE 1 AC4 30 GLY A 213 ALA A 214 LYS A 215 GLY A 237 SITE 2 AC4 30 GLY A 238 LEU A 256 GLY A 312 ASN A 336 SITE 3 AC4 30 PRO A 338 GLY A 340 VAL A 341 GLU A 343 SITE 4 AC4 30 GLY A 371 GLY A 372 GLY A 373 ASP A 374 SITE 5 AC4 30 THR A 375 MG A1417 AF3 A1419 HOH A2397 SITE 6 AC4 30 HOH A2454 HOH A2455 HOH A2456 HOH A2457 SITE 7 AC4 30 HOH A2458 HOH A2459 HOH A2460 HOH A2461 SITE 8 AC4 30 HOH A2462 HOH A3000 SITE 1 AC5 15 ASP A 23 ASN A 25 ARG A 38 HIS A 62 SITE 2 AC5 15 ARG A 65 ARG A 122 GLY A 166 ARG A 170 SITE 3 AC5 15 LYS A 215 AF3 A1419 HOH A2462 HOH A2463 SITE 4 AC5 15 HOH A2464 HOH A2465 HOH A3000 CRYST1 39.380 91.590 108.480 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 0.025394 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009218 0.00000