HEADER ISOMERASE 26-NOV-08 3FDZ
TITLE CRYSTAL STRUCTURE OF PHOSPHOGLYCEROMUTASE FROM BURKHOLDERIA
TITLE 2 PSEUDOMALLEI 1710B WITH BOUND 2,3-DIPHOSPHOGLYCERIC ACID AND 3-
TITLE 3 PHOSPHOGLYCERIC ACID
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 2,3-BISPHOSPHOGLYCERATE-DEPENDENT PHOSPHOGLYCERATE MUTASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PHOSPHOGLYCEROMUTASE, PGAM, BPG-DEPENDENT PGAM, DPGM;
COMPND 5 EC: 5.4.2.1;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: 2,3-BISPHOSPHOGLYCERATE-DEPENDENT PHOSPHOGLYCERATE MUTASE;
COMPND 9 CHAIN: B;
COMPND 10 SYNONYM: PHOSPHOGLYCEROMUTASE, PGAM, BPG-DEPENDENT PGAM, DPGM;
COMPND 11 EC: 5.4.2.1;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA PSEUDOMALLEI 1710B;
SOURCE 3 ORGANISM_TAXID: 320372;
SOURCE 4 STRAIN: 1719B;
SOURCE 5 GENE: BURPS1710B_0662, GPMA;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: AVA0421;
SOURCE 11 MOL_ID: 2;
SOURCE 12 ORGANISM_SCIENTIFIC: BURKHOLDERIA PSEUDOMALLEI 1710B;
SOURCE 13 ORGANISM_TAXID: 320372;
SOURCE 14 STRAIN: 1719B;
SOURCE 15 GENE: BURPS1710B_0662, GPMA;
SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 20 EXPRESSION_SYSTEM_PLASMID: AVA0421
KEYWDS ISOMERASE, SSGCID, PHOSPHOGLYCEROMUTASE, BURKHOLDERIA PSEUDOMALLEI,
KEYWDS 2 GLYCOLYSIS, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER
KEYWDS 3 FOR INFECTIOUS DISEASE
EXPDTA X-RAY DIFFRACTION
AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID)
REVDAT 6 27-DEC-23 3FDZ 1 LINK
REVDAT 5 20-JUL-16 3FDZ 1 HETNAM HETSYN
REVDAT 4 05-OCT-11 3FDZ 1 JRNL VERSN
REVDAT 3 07-APR-09 3FDZ 1 REMARK
REVDAT 2 31-MAR-09 3FDZ 1 REMARK
REVDAT 1 13-JAN-09 3FDZ 0
JRNL AUTH D.R.DAVIES,B.L.STAKER,J.A.ABENDROTH,T.E.EDWARDS,R.HARTLEY,
JRNL AUTH 2 J.LEONARD,H.KIM,A.L.RYCHEL,S.N.HEWITT,P.J.MYLER,L.J.STEWART
JRNL TITL AN ENSEMBLE OF STRUCTURES OF BURKHOLDERIA PSEUDOMALLEI
JRNL TITL 2 2,3-BISPHOSPHOGLYCERATE-DEPENDENT PHOSPHOGLYCERATE MUTASE.
JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 67 1044 2011
JRNL REFN ESSN 1744-3091
JRNL PMID 21904048
JRNL DOI 10.1107/S1744309111030405
REMARK 2
REMARK 2 RESOLUTION. 2.25 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0053
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) : 2.25
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.75
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 20934
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) : 0.187
REMARK 3 R VALUE (WORKING SET) : 0.183
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 : 1066
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) : 2.25
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1440
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.87
REMARK 3 BIN R VALUE (WORKING SET) : 0.2520
REMARK 3 BIN FREE R VALUE SET COUNT : 82
REMARK 3 BIN FREE R VALUE : 0.3310
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3668
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 40
REMARK 3 SOLVENT ATOMS : 223
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 29.18
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.70
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.60000
REMARK 3 B22 (A**2) : -0.45000
REMARK 3 B33 (A**2) : -0.17000
REMARK 3 B12 (A**2) : 0.12000
REMARK 3 B13 (A**2) : -1.14000
REMARK 3 B23 (A**2) : -0.05000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.418
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.266
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.030
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3796 ; 0.013 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5175 ; 1.526 ; 1.974
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 457 ; 6.698 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 177 ;38.445 ;23.390
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 610 ;14.593 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;13.904 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 563 ; 0.091 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2905 ; 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): 2291 ; 0.585 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3693 ; 1.059 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1505 ; 1.923 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1482 ; 3.013 ; 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 : 1.20
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
REMARK 4
REMARK 4 3FDZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-08.
REMARK 100 THE DEPOSITION ID IS D_1000050471.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 30-SEP-08
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 6.00
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : SATURN
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20934
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.07100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4300
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.34500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
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: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.33
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 600, 5% PEG 1000, 10%
REMARK 280 GLYCEROL, 100 MM MES PH 6.0, CRYSTALS SOAKED OVERNIGHT WITH 20
REMARK 280 MM 3-PHOSPHOGLYCERIC ACID, VAPOR DIFFUSION, VAPOR DIFFUSION,
REMARK 280 SITTING DROP, TEMPERATURE 289K, PH 6.00
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, 3
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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS TWO BIOLOGICAL UNITS
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3090 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 18590 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
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: 3
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
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 -7
REMARK 465 ALA A -6
REMARK 465 HIS A -5
REMARK 465 HIS A -4
REMARK 465 HIS A -3
REMARK 465 HIS A -2
REMARK 465 HIS A -1
REMARK 465 HIS A 0
REMARK 465 GLN A 231
REMARK 465 GLU A 232
REMARK 465 ALA A 233
REMARK 465 ILE A 234
REMARK 465 ALA A 235
REMARK 465 LYS A 236
REMARK 465 ALA A 237
REMARK 465 GLN A 238
REMARK 465 ALA A 239
REMARK 465 ALA A 240
REMARK 465 VAL A 241
REMARK 465 ALA A 242
REMARK 465 GLN A 243
REMARK 465 GLN A 244
REMARK 465 GLY A 245
REMARK 465 LYS A 246
REMARK 465 SER A 247
REMARK 465 ALA A 248
REMARK 465 ALA A 249
REMARK 465 MET B -7
REMARK 465 ALA B -6
REMARK 465 HIS B -5
REMARK 465 HIS B -4
REMARK 465 HIS B -3
REMARK 465 HIS B -2
REMARK 465 HIS B -1
REMARK 465 HIS B 0
REMARK 465 ASP B 230
REMARK 465 GLN B 231
REMARK 465 GLU B 232
REMARK 465 ALA B 233
REMARK 465 ILE B 234
REMARK 465 ALA B 235
REMARK 465 LYS B 236
REMARK 465 ALA B 237
REMARK 465 GLN B 238
REMARK 465 ALA B 239
REMARK 465 ALA B 240
REMARK 465 VAL B 241
REMARK 465 ALA B 242
REMARK 465 GLN B 243
REMARK 465 GLN B 244
REMARK 465 GLY B 245
REMARK 465 LYS B 246
REMARK 465 SER B 247
REMARK 465 ALA B 248
REMARK 465 ALA B 249
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 129 CG CD OE1 OE2
REMARK 470 LYS A 140 CG CD CE NZ
REMARK 470 LYS B 140 CG CD CE NZ
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 NE2 GLN A 41 OE1 GLN A 71 2.08
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 ASP A 25 52.32 -95.95
REMARK 500 SER A 166 -60.56 -138.38
REMARK 500 ALA A 181 -137.08 -143.90
REMARK 500 ASP B 25 56.83 -93.88
REMARK 500 SER B 166 -59.07 -127.36
REMARK 500 ALA B 181 -141.56 -141.58
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 DG2 A1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A1002
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PG B1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B1002
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3EZN RELATED DB: PDB
REMARK 900 SAME STRUCTURE WITHOUT LIGANDS
REMARK 900 RELATED ID: BUPSA.00114.A RELATED DB: TARGETDB
REMARK 900 RELATED ID: 3GP3 RELATED DB: PDB
REMARK 900 RELATED ID: 3GP5 RELATED DB: PDB
REMARK 900 RELATED ID: 3GW8 RELATED DB: PDB
DBREF 3FDZ A 1 249 UNP Q3JWH7 GPMA_BURP1 1 249
DBREF 3FDZ B 1 249 UNP Q3JWH7 GPMA_BURP1 1 249
SEQADV 3FDZ MET A -7 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ ALA A -6 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS A -5 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS A -4 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS A -3 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS A -2 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS A -1 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS A 0 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ MET B -7 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ ALA B -6 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS B -5 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS B -4 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS B -3 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS B -2 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS B -1 UNP Q3JWH7 EXPRESSION TAG
SEQADV 3FDZ HIS B 0 UNP Q3JWH7 EXPRESSION TAG
SEQRES 1 A 257 MET ALA HIS HIS HIS HIS HIS HIS MET TYR LYS LEU VAL
SEQRES 2 A 257 LEU ILE ARG HIS GLY GLU SER THR TRP ASN LYS GLU ASN
SEQRES 3 A 257 ARG PHE THR GLY TRP VAL ASP VAL ASP LEU THR GLU GLN
SEQRES 4 A 257 GLY ASN ARG GLU ALA ARG GLN ALA GLY GLN LEU LEU LYS
SEQRES 5 A 257 GLU ALA GLY TYR THR PHE ASP ILE ALA TYR THR SER VAL
SEQRES 6 A 257 LEU LYS ARG ALA ILE ARG THR LEU TRP HIS VAL GLN ASP
SEQRES 7 A 257 GLN MET ASP LEU MET TYR VAL PRO VAL VAL HIS SER TRP
SEQRES 8 A 257 ARG LEU ASN GLU ARG HIS TYR GLY ALA LEU SER GLY LEU
SEQRES 9 A 257 ASN LYS ALA GLU THR ALA ALA LYS TYR GLY ASP GLU GLN
SEQRES 10 A 257 VAL LEU VAL TRP ARG ARG SER TYR ASP THR PRO PRO PRO
SEQRES 11 A 257 ALA LEU GLU PRO GLY ASP GLU ARG ALA PRO TYR ALA ASP
SEQRES 12 A 257 PRO ARG TYR ALA LYS VAL PRO ARG GLU GLN LEU PRO LEU
SEQRES 13 A 257 THR GLU CYS LEU LYS ASP THR VAL ALA ARG VAL LEU PRO
SEQRES 14 A 257 LEU TRP ASN GLU SER ILE ALA PRO ALA VAL LYS ALA GLY
SEQRES 15 A 257 LYS GLN VAL LEU ILE ALA ALA HIS GLY ASN SER LEU ARG
SEQRES 16 A 257 ALA LEU ILE LYS TYR LEU ASP GLY ILE SER ASP ALA ASP
SEQRES 17 A 257 ILE VAL GLY LEU ASN ILE PRO ASN GLY VAL PRO LEU VAL
SEQRES 18 A 257 TYR GLU LEU ASP GLU SER LEU THR PRO ILE ARG HIS TYR
SEQRES 19 A 257 TYR LEU GLY ASP GLN GLU ALA ILE ALA LYS ALA GLN ALA
SEQRES 20 A 257 ALA VAL ALA GLN GLN GLY LYS SER ALA ALA
SEQRES 1 B 257 MET ALA HIS HIS HIS HIS HIS HIS MET TYR LYS LEU VAL
SEQRES 2 B 257 LEU ILE ARG NEP GLY GLU SER THR TRP ASN LYS GLU ASN
SEQRES 3 B 257 ARG PHE THR GLY TRP VAL ASP VAL ASP LEU THR GLU GLN
SEQRES 4 B 257 GLY ASN ARG GLU ALA ARG GLN ALA GLY GLN LEU LEU LYS
SEQRES 5 B 257 GLU ALA GLY TYR THR PHE ASP ILE ALA TYR THR SER VAL
SEQRES 6 B 257 LEU LYS ARG ALA ILE ARG THR LEU TRP HIS VAL GLN ASP
SEQRES 7 B 257 GLN MET ASP LEU MET TYR VAL PRO VAL VAL HIS SER TRP
SEQRES 8 B 257 ARG LEU ASN GLU ARG HIS TYR GLY ALA LEU SER GLY LEU
SEQRES 9 B 257 ASN LYS ALA GLU THR ALA ALA LYS TYR GLY ASP GLU GLN
SEQRES 10 B 257 VAL LEU VAL TRP ARG ARG SER TYR ASP THR PRO PRO PRO
SEQRES 11 B 257 ALA LEU GLU PRO GLY ASP GLU ARG ALA PRO TYR ALA ASP
SEQRES 12 B 257 PRO ARG TYR ALA LYS VAL PRO ARG GLU GLN LEU PRO LEU
SEQRES 13 B 257 THR GLU CYS LEU LYS ASP THR VAL ALA ARG VAL LEU PRO
SEQRES 14 B 257 LEU TRP ASN GLU SER ILE ALA PRO ALA VAL LYS ALA GLY
SEQRES 15 B 257 LYS GLN VAL LEU ILE ALA ALA HIS GLY ASN SER LEU ARG
SEQRES 16 B 257 ALA LEU ILE LYS TYR LEU ASP GLY ILE SER ASP ALA ASP
SEQRES 17 B 257 ILE VAL GLY LEU ASN ILE PRO ASN GLY VAL PRO LEU VAL
SEQRES 18 B 257 TYR GLU LEU ASP GLU SER LEU THR PRO ILE ARG HIS TYR
SEQRES 19 B 257 TYR LEU GLY ASP GLN GLU ALA ILE ALA LYS ALA GLN ALA
SEQRES 20 B 257 ALA VAL ALA GLN GLN GLY LYS SER ALA ALA
MODRES 3FDZ NEP B 9 HIS N1-PHOSPHONOHISTIDINE
HET NEP B 9 14
HET DG2 A1001 15
HET PEG A1002 7
HET 3PG B1001 11
HET PEG B1002 7
HETNAM NEP N1-PHOSPHONOHISTIDINE
HETNAM DG2 (2R)-2,3-DIPHOSPHOGLYCERIC ACID
HETNAM PEG DI(HYDROXYETHYL)ETHER
HETNAM 3PG 3-PHOSPHOGLYCERIC ACID
HETSYN DG2 2,3-BISPHOSPHOGLYCERIC ACID; 2,3-BISPHOSPHOGLYCERATE;
HETSYN 2 DG2 2,3-BPG; 2,3-DIPHOSPHOGLYCERIC ACID; 2,3-
HETSYN 3 DG2 DIPHOSPHOGLYCERATE; 2,3-DPG; (2~{R})-2,3-
HETSYN 4 DG2 DIPHOSPHONOOXYPROPANOIC ACID
FORMUL 2 NEP C6 H10 N3 O5 P
FORMUL 3 DG2 C3 H8 O10 P2
FORMUL 4 PEG 2(C4 H10 O3)
FORMUL 5 3PG C3 H7 O7 P
FORMUL 7 HOH *223(H2 O)
HELIX 1 1 SER A 12 GLU A 17 1 6
HELIX 2 2 THR A 29 ALA A 46 1 18
HELIX 3 3 LEU A 58 ASP A 73 1 16
HELIX 4 4 TRP A 83 ASN A 86 5 4
HELIX 5 5 TYR A 90 SER A 94 5 5
HELIX 6 6 ASN A 97 GLY A 106 1 10
HELIX 7 7 GLY A 106 SER A 116 1 11
HELIX 8 8 ASP A 135 ALA A 139 5 5
HELIX 9 9 PRO A 142 LEU A 146 5 5
HELIX 10 10 CYS A 151 SER A 166 1 16
HELIX 11 11 SER A 166 GLY A 174 1 9
HELIX 12 12 HIS A 182 GLY A 195 1 14
HELIX 13 13 SER A 197 VAL A 202 1 6
HELIX 14 14 SER B 12 GLU B 17 1 6
HELIX 15 15 THR B 29 GLY B 47 1 19
HELIX 16 16 LEU B 58 ASP B 73 1 16
HELIX 17 17 TRP B 83 ASN B 86 5 4
HELIX 18 18 TYR B 90 SER B 94 5 5
HELIX 19 19 ASN B 97 GLY B 106 1 10
HELIX 20 20 GLY B 106 SER B 116 1 11
HELIX 21 21 ASP B 135 ALA B 139 5 5
HELIX 22 22 PRO B 142 LEU B 146 5 5
HELIX 23 23 CYS B 151 SER B 166 1 16
HELIX 24 24 SER B 166 ALA B 173 1 8
HELIX 25 25 HIS B 182 ASP B 194 1 13
SHEET 1 A 6 VAL A 79 HIS A 81 0
SHEET 2 A 6 ILE A 52 THR A 55 1 N THR A 55 O VAL A 80
SHEET 3 A 6 VAL A 177 ALA A 181 1 O LEU A 178 N TYR A 54
SHEET 4 A 6 TYR A 2 ARG A 8 1 N VAL A 5 O ILE A 179
SHEET 5 A 6 LEU A 212 LEU A 216 -1 O LEU A 212 N LEU A 6
SHEET 6 A 6 PRO A 222 TYR A 227 -1 O ILE A 223 N GLU A 215
SHEET 1 B 6 VAL B 79 HIS B 81 0
SHEET 2 B 6 ILE B 52 THR B 55 1 N THR B 55 O VAL B 80
SHEET 3 B 6 VAL B 177 ALA B 181 1 O LEU B 178 N TYR B 54
SHEET 4 B 6 TYR B 2 ARG B 8 1 N VAL B 5 O ILE B 179
SHEET 5 B 6 PRO B 211 LEU B 216 -1 O LEU B 216 N TYR B 2
SHEET 6 B 6 PRO B 222 TYR B 227 -1 O TYR B 226 N VAL B 213
LINK C ARG B 8 N NEP B 9 1555 1555 1.34
LINK C NEP B 9 N GLY B 10 1555 1555 1.32
SITE 1 AC1 17 ARG A 8 HIS A 9 ASN A 15 THR A 21
SITE 2 AC1 17 GLY A 22 ARG A 60 GLU A 87 TYR A 90
SITE 3 AC1 17 LYS A 98 ARG A 114 ARG A 115 HIS A 182
SITE 4 AC1 17 GLY A 183 ASN A 184 HOH A 349 HOH A 350
SITE 5 AC1 17 HOH A 355
SITE 1 AC2 6 ASP A 194 LEU A 204 TYR A 214 HIS A 225
SITE 2 AC2 6 TYR A 227 HOH A 259
SITE 1 AC3 12 NEP B 9 ARG B 19 PHE B 20 THR B 21
SITE 2 AC3 12 GLY B 22 GLU B 87 TYR B 90 LYS B 98
SITE 3 AC3 12 ARG B 114 ARG B 115 ASN B 184 HOH B 330
SITE 1 AC4 6 ILE B 190 LEU B 204 TYR B 214 HIS B 225
SITE 2 AC4 6 TYR B 227 HOH B 366
CRYST1 44.390 48.480 62.090 106.03 91.54 107.50 P 1 1
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 0.022528 0.007103 0.002853 0.00000
SCALE2 0.000000 0.021628 0.006755 0.00000
SCALE3 0.000000 0.000000 0.016879 0.00000