HEADER TRANSFERASE 02-NOV-07 3B8X
TITLE CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXYMANNOSE-3-DEHYDRATASE (COLD)
TITLE 2 H188N MUTANT WITH BOUND GDP-PEROSAMINE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PYRIDOXAMINE 5-PHOSPHATE-DEPENDENT DEHYDRASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: WBDK;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 244320;
SOURCE 4 STRAIN: O55:H7;
SOURCE 5 GENE: WBDK;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28JT
KEYWDS ASPARTATE AMINOTRANSFERASE, COLITOSE, PEROSAMINE, O-ANTIGEN, PLP,
KEYWDS 2 PYRIDOXAL PHOSPHATE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.D.COOK,H.M.HOLDEN
REVDAT 7 30-AUG-23 3B8X 1 REMARK
REVDAT 6 20-OCT-21 3B8X 1 REMARK SEQADV LINK
REVDAT 5 13-JUL-11 3B8X 1 VERSN
REVDAT 4 24-FEB-09 3B8X 1 VERSN
REVDAT 3 19-FEB-08 3B8X 1 JRNL
REVDAT 2 29-JAN-08 3B8X 1 REMARK
REVDAT 1 27-NOV-07 3B8X 0
JRNL AUTH P.D.COOK,H.M.HOLDEN
JRNL TITL GDP-4-KETO-6-DEOXY-D-MANNOSE 3-DEHYDRATASE, ACCOMMODATING A
JRNL TITL 2 SUGAR SUBSTRATE IN THE ACTIVE SITE.
JRNL REF J.BIOL.CHEM. V. 283 4295 2008
JRNL REFN ISSN 0021-9258
JRNL PMID 18045869
JRNL DOI 10.1074/JBC.M708893200
REMARK 2
REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : TNT
REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4
REMARK 3 NUMBER OF REFLECTIONS : 75464
REMARK 3
REMARK 3 USING DATA ABOVE SIGMA CUTOFF.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.177
REMARK 3 R VALUE (WORKING SET) : 0.173
REMARK 3 FREE R VALUE : 0.260
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 7680
REMARK 3
REMARK 3 USING ALL DATA, NO SIGMA CUTOFF.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1770
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 83883
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6198
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 126
REMARK 3 SOLVENT ATOMS : 665
REMARK 3
REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT
REMARK 3 BOND LENGTHS (A) : 0.013 ; NULL ; NULL
REMARK 3 BOND ANGLES (DEGREES) : 1.900 ; NULL ; NULL
REMARK 3 TORSION ANGLES (DEGREES) : 17.500; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL
REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL
REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL
REMARK 3
REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 RESTRAINT LIBRARIES.
REMARK 3 STEREOCHEMISTRY : ENGH & HUBER
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : ISOTROPIC
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3B8X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-07.
REMARK 100 THE DEPOSITION ID IS D_1000045226.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-JUL-07
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
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 : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NI FILTER
REMARK 200 OPTICS : MONTELL OPTICS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : BRUKER
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT
REMARK 200 DATA SCALING SOFTWARE : SAINT, SADABS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75510
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4
REMARK 200 DATA REDUNDANCY : 5.780
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.08500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.2400
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79
REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0
REMARK 200 DATA REDUNDANCY IN SHELL : 2.54
REMARK 200 R MERGE FOR SHELL (I) : 0.40800
REMARK 200 R SYM FOR SHELL (I) : 0.40800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.160
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: EPMR
REMARK 200 STARTING MODEL: 2GMU
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.61
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 3400, 400 MM MGCL2, 100 MM
REMARK 280 MES, 2 MM 2-OXOGLUTARATE, 10 MM GDP-PEROSAMINE, PH 6.0, BATCH,
REMARK 280 TEMPERATURE 298K
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 31.20550
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.97000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.06150
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.97000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.20550
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.06150
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 7390 ANGSTROM**2
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY A -1
REMARK 465 HIS A 0
REMARK 465 MET A 1
REMARK 465 ILE A 2
REMARK 465 GLY B -1
REMARK 465 HIS B 0
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 LEU B 339 CA - CB - CG ANGL. DEV. = -14.4 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 ASP A 12 -166.04 -126.13
REMARK 500 LYS A 26 15.35 58.06
REMARK 500 MET A 30 122.80 -34.82
REMARK 500 SER A 87 -153.50 -173.66
REMARK 500 SER A 87 -153.78 -173.51
REMARK 500 LEU A 112 -0.73 74.78
REMARK 500 THR A 124 -165.19 -124.74
REMARK 500 MET A 193 -69.73 82.30
REMARK 500 PHE A 240 53.56 -115.17
REMARK 500 TRP A 301 70.99 41.36
REMARK 500 VAL A 334 -120.74 44.55
REMARK 500 ASN A 354 -102.77 59.21
REMARK 500 LEU A 387 30.17 -99.01
REMARK 500 MET B 30 121.18 -32.41
REMARK 500 SER B 87 -138.35 -174.98
REMARK 500 LEU B 112 -1.76 75.40
REMARK 500 MET B 193 -70.01 79.42
REMARK 500 HIS B 215 -1.67 64.70
REMARK 500 TRP B 301 75.12 43.94
REMARK 500 VAL B 334 -125.61 46.54
REMARK 500 ASN B 354 -100.28 59.50
REMARK 500 LEU B 387 54.53 -95.12
REMARK 500
REMARK 500 REMARK: NULL
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 NA A 671 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LEU A 6 O
REMARK 620 2 ASN A 371 O 104.2
REMARK 620 3 HOH A 743 O 160.7 95.1
REMARK 620 4 HOH A 744 O 86.2 97.8 90.2
REMARK 620 5 HOH A 872 O 93.8 91.5 86.7 170.4
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 672 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 80 OE2
REMARK 620 2 LYS A 103 NZ 97.1
REMARK 620 3 ALA A 122 O 107.4 72.7
REMARK 620 4 THR A 124 OG1 127.1 124.6 114.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 669 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 THR A 175 O
REMARK 620 2 ASP A 201 OD2 164.4
REMARK 620 3 HOH A 688 O 105.9 89.0
REMARK 620 4 HOH A 751 O 98.0 85.2 94.7
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA B 668 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 PHE A 242 O
REMARK 620 2 ASN B 341 OD1 83.8
REMARK 620 3 ASP B 343 OD1 99.0 107.3
REMARK 620 4 ASP B 343 OD2 96.2 161.2 54.0
REMARK 620 5 HOH B 895 O 169.8 86.8 80.0 91.4
REMARK 620 6 HOH B 959 O 114.3 90.8 143.7 106.1 69.7
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 673 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ARG A 273 NH2
REMARK 620 2 GLN A 373 OE1 115.3
REMARK 620 3 HOH A 831 O 81.3 103.5
REMARK 620 4 HOH A 853 O 101.1 54.9 157.4
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA B 666 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LEU B 6 O
REMARK 620 2 ASN B 371 O 103.4
REMARK 620 3 HOH B 694 O 90.6 91.9
REMARK 620 4 HOH B 722 O 161.0 93.4 79.9
REMARK 620 5 HOH B 745 O 89.0 156.4 67.7 72.2
REMARK 620 6 HOH B 751 O 107.4 89.9 161.0 81.2 105.7
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA B 670 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 THR B 175 O
REMARK 620 2 ASP B 201 OD2 177.5
REMARK 620 3 HOH B 765 O 92.4 85.4
REMARK 620 4 HOH B 798 O 88.8 93.6 165.7
REMARK 620 5 HOH B 859 O 88.4 92.9 90.5 75.3
REMARK 620 6 HOH B 892 O 99.2 79.6 93.1 100.8 171.4
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA B 667 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 378 OD2
REMARK 620 2 HOH B 847 O 78.0
REMARK 620 3 HOH B 912 O 168.8 92.7
REMARK 620 4 HOH B 995 O 69.7 87.4 116.5
REMARK 620 5 HOH B 997 O 72.9 150.9 116.2 82.1
REMARK 620 6 HOH B1000 O 85.9 93.3 88.6 154.9 85.2
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 669
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 671
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 672
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 673
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 666
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 667
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 668
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 670
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE G4M A 500
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 674
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 675
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 676
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE G4M B 500
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2GMU RELATED DB: PDB
REMARK 900 STRUCTURE OF UREE
REMARK 900 RELATED ID: 2R0T RELATED DB: PDB
REMARK 900 STRUCTURE OF GDP-4-KETO-6-DEOXYMANNOSE-3-DEHYDRATASE WITH A TRAPPED
REMARK 900 PLP-GLUTAMATE GEMINAL DIAMINE
DBREF 3B8X A 1 388 UNP Q9F118 Q9F118_ECOLX 1 388
DBREF 3B8X B 1 388 UNP Q9F118 Q9F118_ECOLX 1 388
SEQADV 3B8X GLY A -1 UNP Q9F118 EXPRESSION TAG
SEQADV 3B8X HIS A 0 UNP Q9F118 EXPRESSION TAG
SEQADV 3B8X ASN A 188 UNP Q9F118 HIS 188 ENGINEERED MUTATION
SEQADV 3B8X GLY B -1 UNP Q9F118 EXPRESSION TAG
SEQADV 3B8X HIS B 0 UNP Q9F118 EXPRESSION TAG
SEQADV 3B8X ASN B 188 UNP Q9F118 HIS 188 ENGINEERED MUTATION
SEQRES 1 A 390 GLY HIS MET ILE ASN TYR PRO LEU ALA SER SER THR TRP
SEQRES 2 A 390 ASP ASP LEU GLU TYR LYS ALA ILE GLN SER VAL LEU ASP
SEQRES 3 A 390 SER LYS MET PHE THR MET GLY GLU TYR VAL LYS GLN TYR
SEQRES 4 A 390 GLU THR GLN PHE ALA LYS THR PHE GLY SER LYS TYR ALA
SEQRES 5 A 390 VAL MET VAL SER SER GLY SER THR ALA ASN LEU LEU MET
SEQRES 6 A 390 ILE ALA ALA LEU PHE PHE THR LYS LYS PRO ARG LEU LYS
SEQRES 7 A 390 LYS GLY ASP GLU ILE ILE VAL PRO ALA VAL SER TRP SER
SEQRES 8 A 390 THR THR TYR TYR PRO LEU GLN GLN TYR GLY LEU ARG VAL
SEQRES 9 A 390 LYS PHE VAL ASP ILE ASP ILE ASN THR LEU ASN ILE ASP
SEQRES 10 A 390 ILE GLU SER LEU LYS GLU ALA VAL THR ASP SER THR LYS
SEQRES 11 A 390 ALA ILE LEU THR VAL ASN LEU LEU GLY ASN PRO ASN ASN
SEQRES 12 A 390 PHE ASP GLU ILE ASN LYS ILE ILE GLY GLY ARG ASP ILE
SEQRES 13 A 390 ILE LEU LEU GLU ASP ASN CYS GLU SER MET GLY ALA THR
SEQRES 14 A 390 PHE ASN ASN LYS CYS ALA GLY THR PHE GLY LEU MET GLY
SEQRES 15 A 390 THR PHE SER SER PHE TYR SER ASN HIS ILE ALA THR MET
SEQRES 16 A 390 GLU GLY GLY CYS ILE VAL THR ASP ASP GLU GLU ILE TYR
SEQRES 17 A 390 HIS ILE LEU LEU CYS ILE ARG ALA HIS GLY TRP THR ARG
SEQRES 18 A 390 ASN LEU PRO LYS LYS ASN LYS VAL THR GLY VAL LYS SER
SEQRES 19 A 390 ASP ASP GLN PHE GLU GLU SER PHE LYS PHE VAL LEU PRO
SEQRES 20 A 390 GLY TYR ASN VAL ARG PRO LEU GLU MET SER GLY ALA ILE
SEQRES 21 A 390 GLY ILE GLU GLN LEU LYS LYS LEU PRO ARG PHE ILE SER
SEQRES 22 A 390 VAL ARG ARG LYS ASN ALA GLU TYR PHE LEU ASP LYS PHE
SEQRES 23 A 390 LYS ASP HIS PRO TYR LEU ASP VAL GLN GLN GLU THR GLY
SEQRES 24 A 390 GLU SER SER TRP PHE GLY PHE SER PHE ILE ILE LYS LYS
SEQRES 25 A 390 ASP SER GLY VAL ILE ARG LYS GLN LEU VAL GLU ASN LEU
SEQRES 26 A 390 ASN SER ALA GLY ILE GLU CYS ARG PRO ILE VAL THR GLY
SEQRES 27 A 390 ASN PHE LEU LYS ASN THR ASP VAL LEU LYS TYR PHE ASP
SEQRES 28 A 390 TYR THR VAL HIS ASN ASN VAL ASP ASN ALA GLU TYR LEU
SEQRES 29 A 390 ASP LYS ASN GLY LEU PHE VAL GLY ASN HIS GLN ILE GLU
SEQRES 30 A 390 LEU PHE ASP GLU ILE ASP TYR LEU ARG GLU VAL LEU LYS
SEQRES 1 B 390 GLY HIS MET ILE ASN TYR PRO LEU ALA SER SER THR TRP
SEQRES 2 B 390 ASP ASP LEU GLU TYR LYS ALA ILE GLN SER VAL LEU ASP
SEQRES 3 B 390 SER LYS MET PHE THR MET GLY GLU TYR VAL LYS GLN TYR
SEQRES 4 B 390 GLU THR GLN PHE ALA LYS THR PHE GLY SER LYS TYR ALA
SEQRES 5 B 390 VAL MET VAL SER SER GLY SER THR ALA ASN LEU LEU MET
SEQRES 6 B 390 ILE ALA ALA LEU PHE PHE THR LYS LYS PRO ARG LEU LYS
SEQRES 7 B 390 LYS GLY ASP GLU ILE ILE VAL PRO ALA VAL SER TRP SER
SEQRES 8 B 390 THR THR TYR TYR PRO LEU GLN GLN TYR GLY LEU ARG VAL
SEQRES 9 B 390 LYS PHE VAL ASP ILE ASP ILE ASN THR LEU ASN ILE ASP
SEQRES 10 B 390 ILE GLU SER LEU LYS GLU ALA VAL THR ASP SER THR LYS
SEQRES 11 B 390 ALA ILE LEU THR VAL ASN LEU LEU GLY ASN PRO ASN ASN
SEQRES 12 B 390 PHE ASP GLU ILE ASN LYS ILE ILE GLY GLY ARG ASP ILE
SEQRES 13 B 390 ILE LEU LEU GLU ASP ASN CYS GLU SER MET GLY ALA THR
SEQRES 14 B 390 PHE ASN ASN LYS CYS ALA GLY THR PHE GLY LEU MET GLY
SEQRES 15 B 390 THR PHE SER SER PHE TYR SER ASN HIS ILE ALA THR MET
SEQRES 16 B 390 GLU GLY GLY CYS ILE VAL THR ASP ASP GLU GLU ILE TYR
SEQRES 17 B 390 HIS ILE LEU LEU CYS ILE ARG ALA HIS GLY TRP THR ARG
SEQRES 18 B 390 ASN LEU PRO LYS LYS ASN LYS VAL THR GLY VAL LYS SER
SEQRES 19 B 390 ASP ASP GLN PHE GLU GLU SER PHE LYS PHE VAL LEU PRO
SEQRES 20 B 390 GLY TYR ASN VAL ARG PRO LEU GLU MET SER GLY ALA ILE
SEQRES 21 B 390 GLY ILE GLU GLN LEU LYS LYS LEU PRO ARG PHE ILE SER
SEQRES 22 B 390 VAL ARG ARG LYS ASN ALA GLU TYR PHE LEU ASP LYS PHE
SEQRES 23 B 390 LYS ASP HIS PRO TYR LEU ASP VAL GLN GLN GLU THR GLY
SEQRES 24 B 390 GLU SER SER TRP PHE GLY PHE SER PHE ILE ILE LYS LYS
SEQRES 25 B 390 ASP SER GLY VAL ILE ARG LYS GLN LEU VAL GLU ASN LEU
SEQRES 26 B 390 ASN SER ALA GLY ILE GLU CYS ARG PRO ILE VAL THR GLY
SEQRES 27 B 390 ASN PHE LEU LYS ASN THR ASP VAL LEU LYS TYR PHE ASP
SEQRES 28 B 390 TYR THR VAL HIS ASN ASN VAL ASP ASN ALA GLU TYR LEU
SEQRES 29 B 390 ASP LYS ASN GLY LEU PHE VAL GLY ASN HIS GLN ILE GLU
SEQRES 30 B 390 LEU PHE ASP GLU ILE ASP TYR LEU ARG GLU VAL LEU LYS
HET NA A 669 1
HET NA A 671 1
HET NA A 672 1
HET NA A 673 1
HET G4M A 500 53
HET EDO A 674 4
HET EDO A 675 4
HET EDO A 676 4
HET NA B 666 1
HET NA B 667 1
HET NA B 668 1
HET NA B 670 1
HET G4M B 500 53
HETNAM NA SODIUM ION
HETNAM G4M [(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-
HETNAM 2 G4M YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,
HETNAM 3 G4M 4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-
HETNAM 4 G4M [(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-
HETNAM 5 G4M METHYLTETRAHYDRO-2H-PYRAN-2-YL DIHYDROGEN DIPHOSPHATE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 3 NA 8(NA 1+)
FORMUL 7 G4M 2(C24 H36 N7 O19 P3)
FORMUL 8 EDO 3(C2 H6 O2)
FORMUL 16 HOH *665(H2 O)
HELIX 1 1 ASP A 12 LYS A 26 1 15
HELIX 2 2 GLY A 31 GLY A 46 1 16
HELIX 3 3 SER A 55 LEU A 67 1 13
HELIX 4 4 TRP A 88 TYR A 98 1 11
HELIX 5 5 ASP A 115 VAL A 123 1 9
HELIX 6 6 LEU A 135 ASN A 138 5 4
HELIX 7 7 ASN A 141 GLY A 150 1 10
HELIX 8 8 ASP A 202 ARG A 213 1 12
HELIX 9 9 LEU A 252 LYS A 285 1 34
HELIX 10 10 ILE A 315 ALA A 326 1 12
HELIX 11 11 ASN A 337 LYS A 340 5 4
HELIX 12 12 ASN A 341 LYS A 346 1 6
HELIX 13 13 VAL A 356 ASN A 365 1 10
HELIX 14 14 LEU A 376 LEU A 387 1 12
HELIX 15 15 ASP B 12 LYS B 26 1 15
HELIX 16 16 GLY B 31 GLY B 46 1 16
HELIX 17 17 SER B 55 LEU B 67 1 13
HELIX 18 18 TRP B 88 TYR B 98 1 11
HELIX 19 19 ASP B 115 VAL B 123 1 9
HELIX 20 20 LEU B 135 ASN B 138 5 4
HELIX 21 21 ASN B 141 GLY B 150 1 10
HELIX 22 22 ASP B 202 ARG B 213 1 12
HELIX 23 23 ASP B 234 PHE B 240 1 7
HELIX 24 24 LEU B 252 LYS B 285 1 34
HELIX 25 25 ILE B 315 GLY B 327 1 13
HELIX 26 26 ASN B 337 LYS B 340 5 4
HELIX 27 27 ASN B 341 LYS B 346 1 6
HELIX 28 28 VAL B 356 ASN B 365 1 10
HELIX 29 29 LEU B 376 LEU B 387 1 12
SHEET 1 A 8 TYR A 49 VAL A 53 0
SHEET 2 A 8 GLY A 196 THR A 200 -1 O THR A 200 N TYR A 49
SHEET 3 A 8 MET A 179 SER A 183 -1 N GLY A 180 O VAL A 199
SHEET 4 A 8 ILE A 155 ASP A 159 1 N GLU A 158 O THR A 181
SHEET 5 A 8 THR A 127 VAL A 133 1 N ILE A 130 O LEU A 157
SHEET 6 A 8 GLU A 80 PRO A 84 1 N ILE A 82 O LEU A 131
SHEET 7 A 8 ARG A 101 VAL A 105 1 O LYS A 103 N ILE A 81
SHEET 8 A 8 ASP A 349 VAL A 352 1 O THR A 351 N PHE A 104
SHEET 1 B 2 THR A 167 PHE A 168 0
SHEET 2 B 2 LYS A 171 CYS A 172 -1 O LYS A 171 N PHE A 168
SHEET 1 C 2 LYS A 224 ASN A 225 0
SHEET 2 C 2 GLY A 229 VAL A 230 -1 O GLY A 229 N ASN A 225
SHEET 1 D 3 LEU A 290 VAL A 292 0
SHEET 2 D 3 GLY A 303 ILE A 308 -1 O ILE A 307 N ASP A 291
SHEET 3 D 3 GLY A 366 GLY A 370 -1 O VAL A 369 N PHE A 304
SHEET 1 E 8 TYR B 49 VAL B 53 0
SHEET 2 E 8 GLY B 196 THR B 200 -1 O THR B 200 N TYR B 49
SHEET 3 E 8 MET B 179 SER B 183 -1 N PHE B 182 O CYS B 197
SHEET 4 E 8 ILE B 155 ASP B 159 1 N GLU B 158 O MET B 179
SHEET 5 E 8 THR B 127 VAL B 133 1 N ILE B 130 O ILE B 155
SHEET 6 E 8 GLU B 80 PRO B 84 1 N GLU B 80 O LYS B 128
SHEET 7 E 8 ARG B 101 VAL B 105 1 O LYS B 103 N ILE B 81
SHEET 8 E 8 ASP B 349 VAL B 352 1 O THR B 351 N PHE B 104
SHEET 1 F 2 THR B 167 PHE B 168 0
SHEET 2 F 2 LYS B 171 CYS B 172 -1 O LYS B 171 N PHE B 168
SHEET 1 G 2 LYS B 224 ASN B 225 0
SHEET 2 G 2 GLY B 229 VAL B 230 -1 O GLY B 229 N ASN B 225
SHEET 1 H 4 LEU B 290 ASP B 291 0
SHEET 2 H 4 GLY B 303 ILE B 308 -1 O ILE B 307 N ASP B 291
SHEET 3 H 4 GLY B 366 GLY B 370 -1 O VAL B 369 N PHE B 304
SHEET 4 H 4 CYS B 330 ARG B 331 -1 N ARG B 331 O PHE B 368
LINK O LEU A 6 NA NA A 671 1555 1555 2.47
LINK OE2 GLU A 80 NA NA A 672 1555 1555 2.39
LINK NZ LYS A 103 NA NA A 672 1555 1555 2.66
LINK O ALA A 122 NA NA A 672 1555 1555 2.81
LINK OG1 THR A 124 NA NA A 672 1555 1555 2.45
LINK O THR A 175 NA NA A 669 1555 1555 2.43
LINK OD2 ASP A 201 NA NA A 669 1555 1555 2.67
LINK O PHE A 242 NA NA B 668 1555 1555 2.41
LINK NH2 ARG A 273 NA NA A 673 1555 1555 2.88
LINK O ASN A 371 NA NA A 671 1555 1555 2.59
LINK OE1 GLN A 373 NA NA A 673 1555 1555 2.93
LINK NA NA A 669 O HOH A 688 1555 1555 2.41
LINK NA NA A 669 O HOH A 751 1555 1555 2.48
LINK NA NA A 671 O HOH A 743 1555 1555 2.60
LINK NA NA A 671 O HOH A 744 1555 1555 2.45
LINK NA NA A 671 O HOH A 872 1555 1555 2.38
LINK NA NA A 673 O HOH A 831 1555 1555 2.42
LINK NA NA A 673 O HOH A 853 1555 1555 2.99
LINK O LEU B 6 NA NA B 666 1555 1555 2.45
LINK O THR B 175 NA NA B 670 1555 1555 2.49
LINK OD2 ASP B 201 NA NA B 670 1555 1555 2.66
LINK OD1 ASN B 341 NA NA B 668 1555 1555 2.32
LINK OD1 ASP B 343 NA NA B 668 1555 1555 2.50
LINK OD2 ASP B 343 NA NA B 668 1555 1555 2.35
LINK O ASN B 371 NA NA B 666 1555 1555 2.63
LINK OD2 ASP B 378 NA NA B 667 1555 1555 2.90
LINK NA NA B 666 O HOH B 694 1555 1555 2.42
LINK NA NA B 666 O HOH B 722 1555 1555 2.54
LINK NA NA B 666 O HOH B 745 1555 1555 2.87
LINK NA NA B 666 O HOH B 751 1555 1555 2.32
LINK NA NA B 667 O HOH B 847 1555 1555 2.39
LINK NA NA B 667 O HOH B 912 1555 1555 2.59
LINK NA NA B 667 O HOH B 995 1555 1555 2.39
LINK NA NA B 667 O HOH B 997 1555 1555 2.45
LINK NA NA B 667 O HOH B1000 1555 1555 2.84
LINK NA NA B 668 O HOH B 895 1555 1555 2.46
LINK NA NA B 668 O HOH B 959 1555 1555 2.35
LINK NA NA B 670 O HOH B 765 1555 1555 2.72
LINK NA NA B 670 O HOH B 798 1555 1555 2.52
LINK NA NA B 670 O HOH B 859 1555 1555 2.52
LINK NA NA B 670 O HOH B 892 1555 1555 2.63
SITE 1 AC1 6 THR A 175 ASP A 201 HOH A 688 HOH A 751
SITE 2 AC1 6 HOH B 717 HOH B 747
SITE 1 AC2 5 LEU A 6 ASN A 371 HOH A 743 HOH A 744
SITE 2 AC2 5 HOH A 872
SITE 1 AC3 6 GLU A 80 LYS A 103 ALA A 122 THR A 124
SITE 2 AC3 6 SER A 126 THR A 127
SITE 1 AC4 6 THR A 10 ASN A 188 ARG A 273 GLN A 373
SITE 2 AC4 6 HOH A 831 HOH A 853
SITE 1 AC5 6 LEU B 6 ASN B 371 HOH B 694 HOH B 722
SITE 2 AC5 6 HOH B 745 HOH B 751
SITE 1 AC6 7 GLU B 375 ASP B 378 HOH B 847 HOH B 912
SITE 2 AC6 7 HOH B 995 HOH B 997 HOH B1000
SITE 1 AC7 5 PHE A 242 ASN B 341 ASP B 343 HOH B 895
SITE 2 AC7 5 HOH B 959
SITE 1 AC8 6 THR B 175 ASP B 201 HOH B 765 HOH B 798
SITE 2 AC8 6 HOH B 859 HOH B 892
SITE 1 AC9 30 SER A 55 GLY A 56 SER A 57 ASN A 60
SITE 2 AC9 30 SER A 87 TRP A 88 THR A 91 ASP A 159
SITE 3 AC9 30 CYS A 161 GLU A 162 SER A 183 PHE A 185
SITE 4 AC9 30 TYR A 186 SER A 187 GLU A 329 ARG A 331
SITE 5 AC9 30 HOH A 677 HOH A 756 HOH A 817 HOH A 885
SITE 6 AC9 30 HOH A 914 LYS B 26 MET B 27 PHE B 28
SITE 7 AC9 30 THR B 29 HIS B 215 ARG B 219 PHE B 240
SITE 8 AC9 30 ASN B 248 HOH B 903
SITE 1 BC1 4 GLU A 38 ALA A 50 TYR A 206 HOH A 811
SITE 1 BC2 5 SER A 9 THR A 10 TRP A 11 ARG A 268
SITE 2 BC2 5 GLN A 373
SITE 1 BC3 3 GLY A 78 GLU A 80 ARG A 101
SITE 1 BC4 30 LYS A 26 MET A 27 PHE A 28 THR A 29
SITE 2 BC4 30 HIS A 215 ARG A 219 PHE A 240 ASN A 248
SITE 3 BC4 30 LEU B 6 SER B 55 GLY B 56 SER B 57
SITE 4 BC4 30 TRP B 88 THR B 90 ASP B 159 CYS B 161
SITE 5 BC4 30 GLU B 162 SER B 183 PHE B 185 TYR B 186
SITE 6 BC4 30 SER B 187 GLU B 329 ARG B 331 HOH B 676
SITE 7 BC4 30 HOH B 705 HOH B 742 HOH B 761 HOH B 864
SITE 8 BC4 30 HOH B 866 HOH B 925
CRYST1 62.411 98.123 119.940 90.00 90.00 90.00 P 21 21 21 8
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 0.016023 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010191 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008338 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
