HEADER HYDROLASE 13-JAN-17 5MUF
TITLE CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLYCERATE MUTASE FAMILY MEMBER 5
TITLE 2 (PGAM5) IN ITS ENZYMATICALLY ACTIVE DODECAMERIC FORM INDUCED BY THE
TITLE 3 PRESENCE OF THE N-TERMINAL WDPNWD MOTIF
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN PHOSPHATASE PGAM5, MITOCHONDRIAL;
COMPND 3 CHAIN: A, B, C;
COMPND 4 SYNONYM: BCL-XL-BINDING PROTEIN V68,PHOSPHOGLYCERATE MUTASE FAMILY
COMPND 5 MEMBER 5;
COMPND 6 EC: 3.1.3.16;
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: PGAM5;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: R3-PRARE2;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4
KEYWDS PHOSPHOGLYCERATE MUTASE FAMILY MEMBER 5, PGAM5, SERINE/THREONINE
KEYWDS 2 PHOSPHATASE, MITOCHONDRIAL PROTEIN, HYDROLASE, WDPNWD MOTIF, WDXNWD
KEYWDS 3 MOTIF, DIMER, DODECAMER, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS
KEYWDS 4 CONSORTIUM, SGC
EXPDTA X-RAY DIFFRACTION
AUTHOR A.CHAIKUAD,I.ALFANO,S.PICAUD,P.FILIPPAKOPOULOS,F.VON DELFT,C.BOUNTRA,
AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,S.KNAPP,STRUCTURAL GENOMICS CONSORTIUM
AUTHOR 3 (SGC)
REVDAT 3 17-JAN-24 5MUF 1 REMARK
REVDAT 2 19-JUL-17 5MUF 1
REVDAT 1 12-JUL-17 5MUF 0
JRNL AUTH A.CHAIKUAD,P.FILIPPAKOPOULOS,S.R.MARCSISIN,S.PICAUD,
JRNL AUTH 2 M.SCHRODER,S.SEKINE,H.ICHIJO,J.R.ENGEN,K.TAKEDA,S.KNAPP
JRNL TITL STRUCTURES OF PGAM5 PROVIDE INSIGHT INTO ACTIVE SITE
JRNL TITL 2 PLASTICITY AND MULTIMERIC ASSEMBLY.
JRNL REF STRUCTURE V. 25 1089 2017
JRNL REFN ISSN 1878-4186
JRNL PMID 28648608
JRNL DOI 10.1016/J.STR.2017.05.020
REMARK 2
REMARK 2 RESOLUTION. 3.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0158
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.03
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4
REMARK 3 NUMBER OF REFLECTIONS : 17300
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) : 0.228
REMARK 3 R VALUE (WORKING SET) : 0.226
REMARK 3 FREE R VALUE : 0.256
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 933
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) : 3.11
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1300
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.45
REMARK 3 BIN R VALUE (WORKING SET) : 0.3470
REMARK 3 BIN FREE R VALUE SET COUNT : 78
REMARK 3 BIN FREE R VALUE : 0.3510
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5062
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 15
REMARK 3 SOLVENT ATOMS : 51
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 55.30
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.60
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.49000
REMARK 3 B22 (A**2) : 1.02000
REMARK 3 B33 (A**2) : -1.51000
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): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.451
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.369
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 46.834
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.904
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.868
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5197 ; 0.010 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 4833 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7052 ; 1.104 ; 1.955
REMARK 3 BOND ANGLES OTHERS (DEGREES): 11142 ; 0.779 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 623 ; 6.308 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 252 ;29.083 ;21.905
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 870 ;15.347 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 63 ;13.027 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 764 ; 0.066 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5747 ; 0.005 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1136 ; 0.002 ; 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): 2509 ; 0.623 ; 2.046
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2508 ; 0.623 ; 2.046
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3127 ; 1.156 ; 3.066
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3128 ; 1.156 ; 3.067
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2687 ; 0.466 ; 2.096
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2674 ; 0.462 ; 2.088
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3907 ; 0.881 ; 3.112
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5641 ; 2.385 ;23.145
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5641 ; 2.385 ;23.152
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 NCS TYPE: LOCAL
REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3
REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT
REMARK 3 1 A 56 289 B 56 289 13876 0.05 0.05
REMARK 3 2 A 56 289 C 56 289 13904 0.04 0.05
REMARK 3 3 B 56 289 C 56 289 13842 0.05 0.05
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 3
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 56 A 289
REMARK 3 ORIGIN FOR THE GROUP (A): -0.2105 55.5579 -52.5378
REMARK 3 T TENSOR
REMARK 3 T11: 0.3240 T22: 0.5884
REMARK 3 T33: 0.1150 T12: -0.0153
REMARK 3 T13: -0.0083 T23: 0.0224
REMARK 3 L TENSOR
REMARK 3 L11: 0.3203 L22: 0.7970
REMARK 3 L33: 0.5538 L12: 0.1906
REMARK 3 L13: -0.0066 L23: -0.2755
REMARK 3 S TENSOR
REMARK 3 S11: 0.0058 S12: 0.0341 S13: 0.1621
REMARK 3 S21: -0.0547 S22: 0.0487 S23: 0.0007
REMARK 3 S31: 0.0046 S32: 0.0093 S33: -0.0545
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 : B 56 B 289
REMARK 3 ORIGIN FOR THE GROUP (A): 0.4401 34.4210 -38.5234
REMARK 3 T TENSOR
REMARK 3 T11: 0.3417 T22: 0.6076
REMARK 3 T33: 0.0359 T12: -0.0027
REMARK 3 T13: 0.0107 T23: -0.0136
REMARK 3 L TENSOR
REMARK 3 L11: 0.8439 L22: 0.1638
REMARK 3 L33: 0.6107 L12: 0.0974
REMARK 3 L13: 0.0333 L23: -0.2244
REMARK 3 S TENSOR
REMARK 3 S11: 0.0535 S12: -0.0521 S13: -0.0114
REMARK 3 S21: 0.0173 S22: 0.0246 S23: 0.0261
REMARK 3 S31: 0.0478 S32: 0.0064 S33: -0.0781
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : C 56 C 289
REMARK 3 ORIGIN FOR THE GROUP (A): -0.3577 21.2479 -12.6646
REMARK 3 T TENSOR
REMARK 3 T11: 0.3929 T22: 0.5957
REMARK 3 T33: 0.0262 T12: 0.0331
REMARK 3 T13: -0.0139 T23: -0.0066
REMARK 3 L TENSOR
REMARK 3 L11: 0.9538 L22: 1.5381
REMARK 3 L33: 1.0435 L12: -0.3233
REMARK 3 L13: 0.2844 L23: -0.3114
REMARK 3 S TENSOR
REMARK 3 S11: 0.2046 S12: 0.0768 S13: 0.0265
REMARK 3 S21: -0.0733 S22: -0.0778 S23: -0.0731
REMARK 3 S31: 0.2138 S32: -0.0099 S33: -0.1268
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
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
REMARK 4
REMARK 4 5MUF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-17.
REMARK 100 THE DEPOSITION ID IS D_1200003036.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-APR-11
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 5.7
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I03
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97630
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18243
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100
REMARK 200 RESOLUTION RANGE LOW (A) : 41.030
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3
REMARK 200 DATA REDUNDANCY : 7.000
REMARK 200 R MERGE (I) : 0.27100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.27
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2
REMARK 200 DATA REDUNDANCY IN SHELL : 6.90
REMARK 200 R MERGE FOR SHELL (I) : 0.99300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000
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: 3MXO
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 62.37
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 3350 AND 0.1 M MES, PH 5.7,
REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X,Y,-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.10750
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 70.70150
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 91.56000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.10750
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 70.70150
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 91.56000
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.10750
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 70.70150
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 91.56000
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.10750
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 70.70150
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 91.56000
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: DODECAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 141.40300
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 141.40300
REMARK 350 BIOMT3 4 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 SER A 52
REMARK 465 MET A 53
REMARK 465 GLY A 54
REMARK 465 PRO A 55
REMARK 465 PRO A 67
REMARK 465 LEU A 68
REMARK 465 SER A 69
REMARK 465 LEU A 70
REMARK 465 ILE A 71
REMARK 465 ASN A 72
REMARK 465 VAL A 73
REMARK 465 ARG A 74
REMARK 465 LYS A 75
REMARK 465 ARG A 76
REMARK 465 ASN A 77
REMARK 465 VAL A 78
REMARK 465 GLU A 79
REMARK 465 SER A 80
REMARK 465 GLY A 81
REMARK 465 GLU A 82
REMARK 465 GLU A 83
REMARK 465 GLU A 84
REMARK 465 LEU A 85
REMARK 465 ALA A 86
REMARK 465 SER A 87
REMARK 465 LYS A 88
REMARK 465 LEU A 89
REMARK 465 ASP A 90
REMARK 465 SER B 52
REMARK 465 MET B 53
REMARK 465 GLY B 54
REMARK 465 PRO B 55
REMARK 465 PRO B 67
REMARK 465 LEU B 68
REMARK 465 SER B 69
REMARK 465 LEU B 70
REMARK 465 ILE B 71
REMARK 465 ASN B 72
REMARK 465 VAL B 73
REMARK 465 ARG B 74
REMARK 465 LYS B 75
REMARK 465 ARG B 76
REMARK 465 ASN B 77
REMARK 465 VAL B 78
REMARK 465 GLU B 79
REMARK 465 SER B 80
REMARK 465 GLY B 81
REMARK 465 GLU B 82
REMARK 465 GLU B 83
REMARK 465 GLU B 84
REMARK 465 LEU B 85
REMARK 465 ALA B 86
REMARK 465 SER B 87
REMARK 465 LYS B 88
REMARK 465 LEU B 89
REMARK 465 ASP B 90
REMARK 465 SER C 52
REMARK 465 MET C 53
REMARK 465 GLY C 54
REMARK 465 PRO C 55
REMARK 465 PRO C 67
REMARK 465 LEU C 68
REMARK 465 SER C 69
REMARK 465 LEU C 70
REMARK 465 ILE C 71
REMARK 465 ASN C 72
REMARK 465 VAL C 73
REMARK 465 ARG C 74
REMARK 465 LYS C 75
REMARK 465 ARG C 76
REMARK 465 ASN C 77
REMARK 465 VAL C 78
REMARK 465 GLU C 79
REMARK 465 SER C 80
REMARK 465 GLY C 81
REMARK 465 GLU C 82
REMARK 465 GLU C 83
REMARK 465 GLU C 84
REMARK 465 LEU C 85
REMARK 465 ALA C 86
REMARK 465 SER C 87
REMARK 465 LYS C 88
REMARK 465 LEU C 89
REMARK 465 ASP C 90
REMARK 465 HIS C 91
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLU A 66 CG CD OE1 OE2
REMARK 470 HIS A 91 CG ND1 CD2 CE1 NE2
REMARK 470 GLU B 66 CG CD OE1 OE2
REMARK 470 HIS B 91 CG ND1 CD2 CE1 NE2
REMARK 470 GLU C 66 CG CD OE1 OE2
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 61 59.15 -102.97
REMARK 500 ASP A 63 -64.38 -154.67
REMARK 500 ARG A 64 71.92 -166.61
REMARK 500 TYR A 92 -153.18 -117.22
REMARK 500 HIS A 105 170.84 -57.61
REMARK 500 CYS A 168 131.44 -35.04
REMARK 500 CYS A 229 -128.57 -146.43
REMARK 500 ASN B 61 59.18 -102.93
REMARK 500 ASP B 63 -64.31 -154.16
REMARK 500 ARG B 64 71.64 -166.89
REMARK 500 HIS B 105 171.18 -57.96
REMARK 500 CYS B 168 131.28 -34.95
REMARK 500 CYS B 229 -129.64 -146.33
REMARK 500 ASN C 61 59.15 -102.94
REMARK 500 ASP C 63 -64.10 -154.95
REMARK 500 ARG C 64 71.98 -167.47
REMARK 500 HIS C 105 170.76 -57.80
REMARK 500 CYS C 168 131.30 -34.99
REMARK 500 CYS C 229 -128.50 -146.16
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 PO4 A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 C 301
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3O0T RELATED DB: PDB
REMARK 900 RELATED ID: 3MXO RELATED DB: PDB
DBREF 5MUF A 54 289 UNP Q96HS1 PGAM5_HUMAN 54 289
DBREF 5MUF B 54 289 UNP Q96HS1 PGAM5_HUMAN 54 289
DBREF 5MUF C 54 289 UNP Q96HS1 PGAM5_HUMAN 54 289
SEQADV 5MUF SER A 52 UNP Q96HS1 EXPRESSION TAG
SEQADV 5MUF MET A 53 UNP Q96HS1 EXPRESSION TAG
SEQADV 5MUF SER B 52 UNP Q96HS1 EXPRESSION TAG
SEQADV 5MUF MET B 53 UNP Q96HS1 EXPRESSION TAG
SEQADV 5MUF SER C 52 UNP Q96HS1 EXPRESSION TAG
SEQADV 5MUF MET C 53 UNP Q96HS1 EXPRESSION TAG
SEQRES 1 A 238 SER MET GLY PRO GLY VAL TRP ASP PRO ASN TRP ASP ARG
SEQRES 2 A 238 ARG GLU PRO LEU SER LEU ILE ASN VAL ARG LYS ARG ASN
SEQRES 3 A 238 VAL GLU SER GLY GLU GLU GLU LEU ALA SER LYS LEU ASP
SEQRES 4 A 238 HIS TYR LYS ALA LYS ALA THR ARG HIS ILE PHE LEU ILE
SEQRES 5 A 238 ARG HIS SER GLN TYR HIS VAL ASP GLY SER LEU GLU LYS
SEQRES 6 A 238 ASP ARG THR LEU THR PRO LEU GLY ARG GLU GLN ALA GLU
SEQRES 7 A 238 LEU THR GLY LEU ARG LEU ALA SER LEU GLY LEU LYS PHE
SEQRES 8 A 238 ASN LYS ILE VAL HIS SER SER MET THR ARG ALA ILE GLU
SEQRES 9 A 238 THR THR ASP ILE ILE SER ARG HIS LEU PRO GLY VAL CYS
SEQRES 10 A 238 LYS VAL SER THR ASP LEU LEU ARG GLU GLY ALA PRO ILE
SEQRES 11 A 238 GLU PRO ASP PRO PRO VAL SER HIS TRP LYS PRO GLU ALA
SEQRES 12 A 238 VAL GLN TYR TYR GLU ASP GLY ALA ARG ILE GLU ALA ALA
SEQRES 13 A 238 PHE ARG ASN TYR ILE HIS ARG ALA ASP ALA ARG GLN GLU
SEQRES 14 A 238 GLU ASP SER TYR GLU ILE PHE ILE CYS HIS ALA ASN VAL
SEQRES 15 A 238 ILE ARG TYR ILE VAL CYS ARG ALA LEU GLN PHE PRO PRO
SEQRES 16 A 238 GLU GLY TRP LEU ARG LEU SER LEU ASN ASN GLY SER ILE
SEQRES 17 A 238 THR HIS LEU VAL ILE ARG PRO ASN GLY ARG VAL ALA LEU
SEQRES 18 A 238 ARG THR LEU GLY ASP THR GLY PHE MET PRO PRO ASP LYS
SEQRES 19 A 238 ILE THR ARG SER
SEQRES 1 B 238 SER MET GLY PRO GLY VAL TRP ASP PRO ASN TRP ASP ARG
SEQRES 2 B 238 ARG GLU PRO LEU SER LEU ILE ASN VAL ARG LYS ARG ASN
SEQRES 3 B 238 VAL GLU SER GLY GLU GLU GLU LEU ALA SER LYS LEU ASP
SEQRES 4 B 238 HIS TYR LYS ALA LYS ALA THR ARG HIS ILE PHE LEU ILE
SEQRES 5 B 238 ARG HIS SER GLN TYR HIS VAL ASP GLY SER LEU GLU LYS
SEQRES 6 B 238 ASP ARG THR LEU THR PRO LEU GLY ARG GLU GLN ALA GLU
SEQRES 7 B 238 LEU THR GLY LEU ARG LEU ALA SER LEU GLY LEU LYS PHE
SEQRES 8 B 238 ASN LYS ILE VAL HIS SER SER MET THR ARG ALA ILE GLU
SEQRES 9 B 238 THR THR ASP ILE ILE SER ARG HIS LEU PRO GLY VAL CYS
SEQRES 10 B 238 LYS VAL SER THR ASP LEU LEU ARG GLU GLY ALA PRO ILE
SEQRES 11 B 238 GLU PRO ASP PRO PRO VAL SER HIS TRP LYS PRO GLU ALA
SEQRES 12 B 238 VAL GLN TYR TYR GLU ASP GLY ALA ARG ILE GLU ALA ALA
SEQRES 13 B 238 PHE ARG ASN TYR ILE HIS ARG ALA ASP ALA ARG GLN GLU
SEQRES 14 B 238 GLU ASP SER TYR GLU ILE PHE ILE CYS HIS ALA ASN VAL
SEQRES 15 B 238 ILE ARG TYR ILE VAL CYS ARG ALA LEU GLN PHE PRO PRO
SEQRES 16 B 238 GLU GLY TRP LEU ARG LEU SER LEU ASN ASN GLY SER ILE
SEQRES 17 B 238 THR HIS LEU VAL ILE ARG PRO ASN GLY ARG VAL ALA LEU
SEQRES 18 B 238 ARG THR LEU GLY ASP THR GLY PHE MET PRO PRO ASP LYS
SEQRES 19 B 238 ILE THR ARG SER
SEQRES 1 C 238 SER MET GLY PRO GLY VAL TRP ASP PRO ASN TRP ASP ARG
SEQRES 2 C 238 ARG GLU PRO LEU SER LEU ILE ASN VAL ARG LYS ARG ASN
SEQRES 3 C 238 VAL GLU SER GLY GLU GLU GLU LEU ALA SER LYS LEU ASP
SEQRES 4 C 238 HIS TYR LYS ALA LYS ALA THR ARG HIS ILE PHE LEU ILE
SEQRES 5 C 238 ARG HIS SER GLN TYR HIS VAL ASP GLY SER LEU GLU LYS
SEQRES 6 C 238 ASP ARG THR LEU THR PRO LEU GLY ARG GLU GLN ALA GLU
SEQRES 7 C 238 LEU THR GLY LEU ARG LEU ALA SER LEU GLY LEU LYS PHE
SEQRES 8 C 238 ASN LYS ILE VAL HIS SER SER MET THR ARG ALA ILE GLU
SEQRES 9 C 238 THR THR ASP ILE ILE SER ARG HIS LEU PRO GLY VAL CYS
SEQRES 10 C 238 LYS VAL SER THR ASP LEU LEU ARG GLU GLY ALA PRO ILE
SEQRES 11 C 238 GLU PRO ASP PRO PRO VAL SER HIS TRP LYS PRO GLU ALA
SEQRES 12 C 238 VAL GLN TYR TYR GLU ASP GLY ALA ARG ILE GLU ALA ALA
SEQRES 13 C 238 PHE ARG ASN TYR ILE HIS ARG ALA ASP ALA ARG GLN GLU
SEQRES 14 C 238 GLU ASP SER TYR GLU ILE PHE ILE CYS HIS ALA ASN VAL
SEQRES 15 C 238 ILE ARG TYR ILE VAL CYS ARG ALA LEU GLN PHE PRO PRO
SEQRES 16 C 238 GLU GLY TRP LEU ARG LEU SER LEU ASN ASN GLY SER ILE
SEQRES 17 C 238 THR HIS LEU VAL ILE ARG PRO ASN GLY ARG VAL ALA LEU
SEQRES 18 C 238 ARG THR LEU GLY ASP THR GLY PHE MET PRO PRO ASP LYS
SEQRES 19 C 238 ILE THR ARG SER
HET PO4 A 301 5
HET PO4 B 301 5
HET PO4 C 301 5
HETNAM PO4 PHOSPHATE ION
FORMUL 4 PO4 3(O4 P 3-)
FORMUL 7 HOH *51(H2 O)
HELIX 1 AA1 LEU A 114 ARG A 118 5 5
HELIX 2 AA2 THR A 121 LEU A 138 1 18
HELIX 3 AA3 MET A 150 LEU A 164 1 15
HELIX 4 AA4 GLU A 193 ILE A 212 1 20
HELIX 5 AA5 HIS A 230 LEU A 242 1 13
HELIX 6 AA6 PRO A 245 LEU A 252 5 8
HELIX 7 AA7 PRO A 282 ILE A 286 5 5
HELIX 8 AA8 LEU B 114 ARG B 118 5 5
HELIX 9 AA9 THR B 121 LEU B 138 1 18
HELIX 10 AB1 MET B 150 LEU B 164 1 15
HELIX 11 AB2 GLU B 193 ILE B 212 1 20
HELIX 12 AB3 HIS B 230 LEU B 242 1 13
HELIX 13 AB4 PRO B 245 LEU B 252 5 8
HELIX 14 AB5 PRO B 282 ILE B 286 5 5
HELIX 15 AB6 LEU C 114 ARG C 118 5 5
HELIX 16 AB7 THR C 121 LEU C 138 1 18
HELIX 17 AB8 MET C 150 LEU C 164 1 15
HELIX 18 AB9 GLU C 193 ILE C 212 1 20
HELIX 19 AC1 HIS C 230 LEU C 242 1 13
HELIX 20 AC2 PRO C 245 LEU C 252 5 8
HELIX 21 AC3 PRO C 282 ILE C 286 5 5
SHEET 1 AA1 6 CYS A 168 THR A 172 0
SHEET 2 AA1 6 LYS A 144 SER A 148 1 N ILE A 145 O CYS A 168
SHEET 3 AA1 6 SER A 223 CYS A 229 1 O ILE A 226 N VAL A 146
SHEET 4 AA1 6 ARG A 98 ARG A 104 1 N ILE A 103 O PHE A 227
SHEET 5 AA1 6 ILE A 259 ILE A 264 -1 O LEU A 262 N ILE A 100
SHEET 6 AA1 6 VAL A 270 ASP A 277 -1 O ALA A 271 N VAL A 263
SHEET 1 AA2 6 CYS B 168 THR B 172 0
SHEET 2 AA2 6 LYS B 144 SER B 148 1 N ILE B 145 O CYS B 168
SHEET 3 AA2 6 SER B 223 CYS B 229 1 O ILE B 226 N VAL B 146
SHEET 4 AA2 6 ARG B 98 ARG B 104 1 N ILE B 103 O PHE B 227
SHEET 5 AA2 6 ILE B 259 ILE B 264 -1 O LEU B 262 N ILE B 100
SHEET 6 AA2 6 VAL B 270 ASP B 277 -1 O ALA B 271 N VAL B 263
SHEET 1 AA3 6 CYS C 168 THR C 172 0
SHEET 2 AA3 6 LYS C 144 SER C 148 1 N ILE C 145 O CYS C 168
SHEET 3 AA3 6 SER C 223 CYS C 229 1 O ILE C 226 N VAL C 146
SHEET 4 AA3 6 ARG C 98 ARG C 104 1 N ILE C 103 O PHE C 227
SHEET 5 AA3 6 ILE C 259 ILE C 264 -1 O LEU C 262 N ILE C 100
SHEET 6 AA3 6 VAL C 270 ASP C 277 -1 O ALA C 271 N VAL C 263
CISPEP 1 ASP A 184 PRO A 185 0 0.41
CISPEP 2 ASP B 184 PRO B 185 0 0.26
CISPEP 3 ASP C 184 PRO C 185 0 1.65
SITE 1 AC1 7 ARG A 104 HIS A 105 ARG A 152 GLU A 177
SITE 2 AC1 7 HIS A 230 ALA A 231 HOH A 411
SITE 1 AC2 7 ARG B 104 HIS B 105 ARG B 152 GLU B 177
SITE 2 AC2 7 HIS B 230 ALA B 231 HOH B 411
SITE 1 AC3 6 ARG C 104 HIS C 105 ARG C 152 GLU C 177
SITE 2 AC3 6 HIS C 230 ALA C 231
CRYST1 82.215 141.403 183.120 90.00 90.00 90.00 I 2 2 2 24
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 0.012163 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007072 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005461 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
