HEADER OXIDOREDUCTASE 04-JAN-07 2JCX
TITLE X-RAY STRUCTURE OF MUTANT 1-DEOXY-D-XYLULOSE 5-PHOSPHATE
TITLE 2 REDUCTOISOMERASE, DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN
TITLE 3 COMPLEX WITH FOSMIDOMYCIN AND NADPH
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: RESIDUES 2-389;
COMPND 5 SYNONYM: DXP REDUCTOISOMERASE, 1-DEOXYXYLULOSE-5-PHOSPHATE
COMPND 6 REDUCTOISOMERASE, 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE SYNTHASE;
COMPND 7 EC: 1.1.1.267;
COMPND 8 ENGINEERED: YES;
COMPND 9 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS;
SOURCE 3 ORGANISM_TAXID: 83332;
SOURCE 4 STRAIN: H37RV;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET101D-TOPO
KEYWDS OXIDOREDUCTASE, DOXP/MEP PATHWAY, ISOPRENE BIOSYNTHESIS, 1-DEOXY-D-
KEYWDS 2 XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, NADP, RV2870C, METAL-BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR L.M.HENRIKSSON,T.UNGE,T.A.JONES,S.L.MOWBRAY
REVDAT 5 13-DEC-23 2JCX 1 REMARK
REVDAT 4 24-FEB-09 2JCX 1 VERSN
REVDAT 3 10-JUL-07 2JCX 1 JRNL
REVDAT 2 22-MAY-07 2JCX 1 JRNL HETATM
REVDAT 1 08-MAY-07 2JCX 0
JRNL AUTH L.M.HENRIKSSON,T.UNGE,J.CARLSSON,J.AQVIST,S.L.MOWBRAY,
JRNL AUTH 2 T.A.JONES
JRNL TITL STRUCTURES OF MYCOBACTERIUM TUBERCULOSIS 1-DEOXY-D-
JRNL TITL 2 XYLULOSE-5-PHOSPHATE REDUCTOISOMERASE PROVIDE NEW INSIGHTS
JRNL TITL 3 INTO CATALYSIS.
JRNL REF J.BIOL.CHEM. V. 282 19905 2007
JRNL REFN ISSN 0021-9258
JRNL PMID 17491006
JRNL DOI 10.1074/JBC.M701935200
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
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) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 3 NUMBER OF REFLECTIONS : 40602
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) : 0.180
REMARK 3 R VALUE (WORKING SET) : 0.178
REMARK 3 FREE R VALUE : 0.215
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2156
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) : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2774
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.1960
REMARK 3 BIN FREE R VALUE SET COUNT : 117
REMARK 3 BIN FREE R VALUE : 0.2570
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5562
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 117
REMARK 3 SOLVENT ATOMS : 440
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.64
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.08000
REMARK 3 B22 (A**2) : 1.32000
REMARK 3 B33 (A**2) : -1.48000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.18000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.235
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.179
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5787 ; 0.011 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7924 ; 1.266 ; 1.967
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 762 ; 5.331 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 231 ;36.095 ;23.593
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 845 ;14.101 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;20.192 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 928 ; 0.079 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4395 ; 0.004 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2775 ; 0.195 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3983 ; 0.294 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 424 ; 0.148 ; 0.200
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): 77 ; 0.188 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.171 ; 0.200
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): 3776 ; 0.571 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6029 ; 1.065 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2011 ; 1.725 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1895 ; 2.779 ; 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 : 1.40
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. THIS ENTRY CONTAINS ATOMS WITH REFINED B- FACTORS AND
REMARK 3 ZERO OCCUPANCY.
REMARK 4
REMARK 4 2JCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JAN-07.
REMARK 100 THE DEPOSITION ID IS D_1290030885.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-MAR-06
REMARK 200 TEMPERATURE (KELVIN) : 110.0
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-4
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.940
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
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 : 42772
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 4.000
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.20000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 2C82
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.50
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.66150
REMARK 290 SMTRY3 2 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: PQS
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 400
REMARK 400 COMPOUND
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 151 TO ASN
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 222 TO GLN
REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASP 151 TO ASN
REMARK 400 ENGINEERED RESIDUE IN CHAIN B, GLU 222 TO GLN
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 THR A -8
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 VAL A 1
REMARK 465 THR A 2
REMARK 465 ASN A 3
REMARK 465 SER A 4
REMARK 465 THR A 5
REMARK 465 ASP A 6
REMARK 465 GLY A 7
REMARK 465 ARG A 8
REMARK 465 ALA A 9
REMARK 465 ASP A 10
REMARK 465 THR B -8
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 VAL B 1
REMARK 465 THR B 2
REMARK 465 ASN B 3
REMARK 465 SER B 4
REMARK 465 THR B 5
REMARK 465 ASP B 6
REMARK 465 GLY B 7
REMARK 465 ARG B 8
REMARK 465 ALA B 9
REMARK 465 ASP B 10
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 O3D NDP B 1390 O HOH B 2233 1.66
REMARK 500 O HOH B 2086 O HOH B 2233 2.16
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 LEU B 108 CA - CB - CG ANGL. DEV. = 14.0 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 127 80.63 -69.89
REMARK 500 SER A 249 171.49 167.17
REMARK 500 ASP A 266 111.01 -162.74
REMARK 500 ALA B 197 38.66 -79.32
REMARK 500 SER B 249 171.39 162.43
REMARK 500 ASP B 266 109.12 -176.89
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 A2077 DISTANCE = 6.08 ANGSTROMS
REMARK 615
REMARK 615 ZERO OCCUPANCY ATOM
REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 615 M RES C SSEQI
REMARK 615 NDP A 1391
REMARK 615 NDP B 1390
REMARK 650
REMARK 650 HELIX
REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1392
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1391
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOM A1390
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A1391
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B1390
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2C82 RELATED DB: PDB
REMARK 900 X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5 -PHOSPHATE REDUCTOISOMERASE,
REMARK 900 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS
REMARK 900 RELATED ID: 2JCV RELATED DB: PDB
REMARK 900 X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5 -PHOSPHATE REDUCTOISOMERASE,
REMARK 900 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH
REMARK 900 FOSMIDOMYCIN AND NADPH
REMARK 900 RELATED ID: 2JCY RELATED DB: PDB
REMARK 900 X-RAY STRUCTURE OF MUTANT 1-DEOXY-D- XYLULOSE 5-PHOSPHATE
REMARK 900 REDUCTOISOMERASE, DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS
REMARK 900 RELATED ID: 2JCZ RELATED DB: PDB
REMARK 900 X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5 -PHOSPHATE REDUCTOISOMERASE,
REMARK 900 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH
REMARK 900 FOSMIDOMYCIN, MANGANESE AND NADPH
REMARK 900 RELATED ID: 2JD0 RELATED DB: PDB
REMARK 900 X-RAY STRUCTURE OF MUTANT 1-DEOXY-D- XYLULOSE 5-PHOSPHATE
REMARK 900 REDUCTOISOMERASE, DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN
REMARK 900 COMPLEX WITH NADPH
REMARK 900 RELATED ID: 2JD1 RELATED DB: PDB
REMARK 900 X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5 -PHOSPHATE REDUCTOISOMERASE,
REMARK 900 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH
REMARK 900 MANGANESE AND NADPH
REMARK 900 RELATED ID: 2JD2 RELATED DB: PDB
REMARK 900 X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5 -PHOSPHATE REDUCTOISOMERASE,
REMARK 900 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH
REMARK 900 MANGANESE
DBREF 2JCX A -8 1 PDB 2JCX 2JCX -8 1
DBREF 2JCX A 2 389 UNP P64012 DXR_MYCTU 2 389
DBREF 2JCX B -8 1 PDB 2JCX 2JCX -8 1
DBREF 2JCX B 2 389 UNP P64012 DXR_MYCTU 2 389
SEQADV 2JCX ASN A 151 UNP P64012 ASP 151 ENGINEERED MUTATION
SEQADV 2JCX GLN A 222 UNP P64012 GLU 222 ENGINEERED MUTATION
SEQADV 2JCX ASN B 151 UNP P64012 ASP 151 ENGINEERED MUTATION
SEQADV 2JCX GLN B 222 UNP P64012 GLU 222 ENGINEERED MUTATION
SEQRES 1 A 398 THR MET ALA HIS HIS HIS HIS HIS HIS VAL THR ASN SER
SEQRES 2 A 398 THR ASP GLY ARG ALA ASP GLY ARG LEU ARG VAL VAL VAL
SEQRES 3 A 398 LEU GLY SER THR GLY SER ILE GLY THR GLN ALA LEU GLN
SEQRES 4 A 398 VAL ILE ALA ASP ASN PRO ASP ARG PHE GLU VAL VAL GLY
SEQRES 5 A 398 LEU ALA ALA GLY GLY ALA HIS LEU ASP THR LEU LEU ARG
SEQRES 6 A 398 GLN ARG ALA GLN THR GLY VAL THR ASN ILE ALA VAL ALA
SEQRES 7 A 398 ASP GLU HIS ALA ALA GLN ARG VAL GLY ASP ILE PRO TYR
SEQRES 8 A 398 HIS GLY SER ASP ALA ALA THR ARG LEU VAL GLU GLN THR
SEQRES 9 A 398 GLU ALA ASP VAL VAL LEU ASN ALA LEU VAL GLY ALA LEU
SEQRES 10 A 398 GLY LEU ARG PRO THR LEU ALA ALA LEU LYS THR GLY ALA
SEQRES 11 A 398 ARG LEU ALA LEU ALA ASN LYS GLU SER LEU VAL ALA GLY
SEQRES 12 A 398 GLY SER LEU VAL LEU ARG ALA ALA ARG PRO GLY GLN ILE
SEQRES 13 A 398 VAL PRO VAL ASN SER GLU HIS SER ALA LEU ALA GLN CYS
SEQRES 14 A 398 LEU ARG GLY GLY THR PRO ASP GLU VAL ALA LYS LEU VAL
SEQRES 15 A 398 LEU THR ALA SER GLY GLY PRO PHE ARG GLY TRP SER ALA
SEQRES 16 A 398 ALA ASP LEU GLU HIS VAL THR PRO GLU GLN ALA GLY ALA
SEQRES 17 A 398 HIS PRO THR TRP SER MET GLY PRO MET ASN THR LEU ASN
SEQRES 18 A 398 SER ALA SER LEU VAL ASN LYS GLY LEU GLN VAL ILE GLU
SEQRES 19 A 398 THR HIS LEU LEU PHE GLY ILE PRO TYR ASP ARG ILE ASP
SEQRES 20 A 398 VAL VAL VAL HIS PRO GLN SER ILE ILE HIS SER MET VAL
SEQRES 21 A 398 THR PHE ILE ASP GLY SER THR ILE ALA GLN ALA SER PRO
SEQRES 22 A 398 PRO ASP MET LYS LEU PRO ILE SER LEU ALA LEU GLY TRP
SEQRES 23 A 398 PRO ARG ARG VAL SER GLY ALA ALA ALA ALA CYS ASP PHE
SEQRES 24 A 398 HIS THR ALA SER SER TRP GLU PHE GLU PRO LEU ASP THR
SEQRES 25 A 398 ASP VAL PHE PRO ALA VAL GLU LEU ALA ARG GLN ALA GLY
SEQRES 26 A 398 VAL ALA GLY GLY CYS MET THR ALA VAL TYR ASN ALA ALA
SEQRES 27 A 398 ASN GLU GLU ALA ALA ALA ALA PHE LEU ALA GLY ARG ILE
SEQRES 28 A 398 GLY PHE PRO ALA ILE VAL GLY ILE ILE ALA ASP VAL LEU
SEQRES 29 A 398 HIS ALA ALA ASP GLN TRP ALA VAL GLU PRO ALA THR VAL
SEQRES 30 A 398 ASP ASP VAL LEU ASP ALA GLN ARG TRP ALA ARG GLU ARG
SEQRES 31 A 398 ALA GLN ARG ALA VAL SER GLY MET
SEQRES 1 B 398 THR MET ALA HIS HIS HIS HIS HIS HIS VAL THR ASN SER
SEQRES 2 B 398 THR ASP GLY ARG ALA ASP GLY ARG LEU ARG VAL VAL VAL
SEQRES 3 B 398 LEU GLY SER THR GLY SER ILE GLY THR GLN ALA LEU GLN
SEQRES 4 B 398 VAL ILE ALA ASP ASN PRO ASP ARG PHE GLU VAL VAL GLY
SEQRES 5 B 398 LEU ALA ALA GLY GLY ALA HIS LEU ASP THR LEU LEU ARG
SEQRES 6 B 398 GLN ARG ALA GLN THR GLY VAL THR ASN ILE ALA VAL ALA
SEQRES 7 B 398 ASP GLU HIS ALA ALA GLN ARG VAL GLY ASP ILE PRO TYR
SEQRES 8 B 398 HIS GLY SER ASP ALA ALA THR ARG LEU VAL GLU GLN THR
SEQRES 9 B 398 GLU ALA ASP VAL VAL LEU ASN ALA LEU VAL GLY ALA LEU
SEQRES 10 B 398 GLY LEU ARG PRO THR LEU ALA ALA LEU LYS THR GLY ALA
SEQRES 11 B 398 ARG LEU ALA LEU ALA ASN LYS GLU SER LEU VAL ALA GLY
SEQRES 12 B 398 GLY SER LEU VAL LEU ARG ALA ALA ARG PRO GLY GLN ILE
SEQRES 13 B 398 VAL PRO VAL ASN SER GLU HIS SER ALA LEU ALA GLN CYS
SEQRES 14 B 398 LEU ARG GLY GLY THR PRO ASP GLU VAL ALA LYS LEU VAL
SEQRES 15 B 398 LEU THR ALA SER GLY GLY PRO PHE ARG GLY TRP SER ALA
SEQRES 16 B 398 ALA ASP LEU GLU HIS VAL THR PRO GLU GLN ALA GLY ALA
SEQRES 17 B 398 HIS PRO THR TRP SER MET GLY PRO MET ASN THR LEU ASN
SEQRES 18 B 398 SER ALA SER LEU VAL ASN LYS GLY LEU GLN VAL ILE GLU
SEQRES 19 B 398 THR HIS LEU LEU PHE GLY ILE PRO TYR ASP ARG ILE ASP
SEQRES 20 B 398 VAL VAL VAL HIS PRO GLN SER ILE ILE HIS SER MET VAL
SEQRES 21 B 398 THR PHE ILE ASP GLY SER THR ILE ALA GLN ALA SER PRO
SEQRES 22 B 398 PRO ASP MET LYS LEU PRO ILE SER LEU ALA LEU GLY TRP
SEQRES 23 B 398 PRO ARG ARG VAL SER GLY ALA ALA ALA ALA CYS ASP PHE
SEQRES 24 B 398 HIS THR ALA SER SER TRP GLU PHE GLU PRO LEU ASP THR
SEQRES 25 B 398 ASP VAL PHE PRO ALA VAL GLU LEU ALA ARG GLN ALA GLY
SEQRES 26 B 398 VAL ALA GLY GLY CYS MET THR ALA VAL TYR ASN ALA ALA
SEQRES 27 B 398 ASN GLU GLU ALA ALA ALA ALA PHE LEU ALA GLY ARG ILE
SEQRES 28 B 398 GLY PHE PRO ALA ILE VAL GLY ILE ILE ALA ASP VAL LEU
SEQRES 29 B 398 HIS ALA ALA ASP GLN TRP ALA VAL GLU PRO ALA THR VAL
SEQRES 30 B 398 ASP ASP VAL LEU ASP ALA GLN ARG TRP ALA ARG GLU ARG
SEQRES 31 B 398 ALA GLN ARG ALA VAL SER GLY MET
HET FOM A1390 11
HET NDP A1391 48
HET SO4 A1392 5
HET NDP B1390 48
HET SO4 B1391 5
HETNAM FOM 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID
HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
HETNAM 2 NDP PHOSPHATE
HETNAM SO4 SULFATE ION
HETSYN FOM FOSMIDOMYCIN
FORMUL 3 FOM C4 H10 N O5 P
FORMUL 4 NDP 2(C21 H30 N7 O17 P3)
FORMUL 5 SO4 2(O4 S 2-)
FORMUL 8 HOH *440(H2 O)
HELIX 1 1 GLY A 22 ASP A 34 1 13
HELIX 2 2 LEU A 51 THR A 61 1 11
HELIX 3 3 ASP A 70 VAL A 77 1 8
HELIX 4 4 ASP A 86 GLN A 94 1 9
HELIX 5 5 LEU A 108 LYS A 118 1 11
HELIX 6 6 LYS A 128 ALA A 133 1 6
HELIX 7 7 GLY A 135 ALA A 141 1 7
HELIX 8 8 ASN A 151 GLY A 163 1 13
HELIX 9 9 SER A 185 GLU A 190 1 6
HELIX 10 10 THR A 193 ALA A 197 1 5
HELIX 11 11 GLY A 206 ALA A 214 1 9
HELIX 12 12 LEU A 216 PHE A 230 1 15
HELIX 13 13 MET A 267 LEU A 275 1 9
HELIX 14 14 PRO A 307 ALA A 318 1 12
HELIX 15 15 CYS A 321 LEU A 338 1 18
HELIX 16 16 GLY A 343 ALA A 357 1 15
HELIX 17 17 VAL A 368 SER A 387 1 20
HELIX 18 18 GLY B 22 ASP B 34 1 13
HELIX 19 19 LEU B 51 THR B 61 1 11
HELIX 20 20 ASP B 70 VAL B 77 1 8
HELIX 21 21 ASP B 86 GLN B 94 1 9
HELIX 22 22 LEU B 108 LYS B 118 1 11
HELIX 23 23 LYS B 128 ALA B 133 1 6
HELIX 24 24 GLY B 135 ALA B 141 1 7
HELIX 25 25 ASN B 151 GLY B 163 1 13
HELIX 26 26 SER B 185 GLU B 190 1 6
HELIX 27 27 THR B 193 ALA B 197 1 5
HELIX 28 28 GLY B 206 ALA B 214 1 9
HELIX 29 29 LEU B 216 PHE B 230 1 15
HELIX 30 30 MET B 267 LEU B 275 1 9
HELIX 31 31 PRO B 307 ALA B 318 1 12
HELIX 32 32 CYS B 321 LEU B 338 1 18
HELIX 33 33 GLY B 343 ALA B 357 1 15
HELIX 34 34 VAL B 368 SER B 387 1 20
SHEET 1 AA 7 TYR A 82 HIS A 83 0
SHEET 2 AA 7 ASN A 65 VAL A 68 1 O ILE A 66 N TYR A 82
SHEET 3 AA 7 ARG A 38 ALA A 46 1 O LEU A 44 N ALA A 67
SHEET 4 AA 7 LEU A 13 LEU A 18 1 O LEU A 13 N GLU A 40
SHEET 5 AA 7 ASP A 98 ASN A 102 1 O VAL A 99 N VAL A 16
SHEET 6 AA 7 ALA A 121 LEU A 125 1 O ARG A 122 N VAL A 100
SHEET 7 AA 7 GLN A 146 PRO A 149 1 O VAL A 148 N LEU A 125
SHEET 1 AB 8 ARG A 236 VAL A 241 0
SHEET 2 AB 8 ALA A 170 ALA A 176 1 O LEU A 172 N ASP A 238
SHEET 3 AB 8 MET A 250 PHE A 253 -1 O MET A 250 N VAL A 173
SHEET 4 AB 8 SER A 257 ALA A 262 -1 O ILE A 259 N VAL A 251
SHEET 5 AB 8 SER B 257 ALA B 262 -1 O THR B 258 N ALA A 262
SHEET 6 AB 8 MET B 250 PHE B 253 -1 N MET B 250 O ILE B 259
SHEET 7 AB 8 ALA B 170 ALA B 176 -1 N ALA B 170 O THR B 252
SHEET 8 AB 8 ARG B 236 VAL B 241 1 O ASP B 238 N LEU B 174
SHEET 1 AC 2 ALA A 293 PHE A 298 0
SHEET 2 AC 2 ALA B 293 PHE B 298 -1 O SER B 294 N PHE A 298
SHEET 1 BA 7 TYR B 82 HIS B 83 0
SHEET 2 BA 7 ASN B 65 VAL B 68 1 O ILE B 66 N TYR B 82
SHEET 3 BA 7 ARG B 38 ALA B 46 1 O LEU B 44 N ALA B 67
SHEET 4 BA 7 LEU B 13 LEU B 18 1 O LEU B 13 N GLU B 40
SHEET 5 BA 7 ASP B 98 ASN B 102 1 O VAL B 99 N VAL B 16
SHEET 6 BA 7 ALA B 121 LEU B 125 1 O ARG B 122 N VAL B 100
SHEET 7 BA 7 GLN B 146 PRO B 149 1 O VAL B 148 N LEU B 125
CISPEP 1 TRP A 277 PRO A 278 0 4.98
CISPEP 2 TRP B 277 PRO B 278 0 6.12
SITE 1 AC1 5 ARG A 162 TRP A 277 PRO A 278 HOH A2092
SITE 2 AC1 5 HOH A2202
SITE 1 AC2 8 ALA B 176 SER B 177 SER B 213 ASN B 218
SITE 2 AC2 8 LYS B 219 HOH B2236 HOH B2237 HOH B2238
SITE 1 AC3 14 SER A 152 GLU A 153 ALA A 176 SER A 177
SITE 2 AC3 14 HIS A 200 TRP A 203 SER A 213 ASN A 218
SITE 3 AC3 14 LYS A 219 GLN A 222 MET A 267 HOH A2193
SITE 4 AC3 14 HOH A2194 HOH A2195
SITE 1 AC4 27 GLY A 19 THR A 21 GLY A 22 SER A 23
SITE 2 AC4 27 ILE A 24 ALA A 46 GLY A 47 GLY A 48
SITE 3 AC4 27 ALA A 49 HIS A 50 ALA A 69 ALA A 103
SITE 4 AC4 27 LEU A 104 LEU A 108 ALA A 126 ASN A 127
SITE 5 AC4 27 LYS A 128 GLU A 129 GLY A 206 ASN A 209
SITE 6 AC4 27 HOH A2001 HOH A2196 HOH A2197 HOH A2198
SITE 7 AC4 27 HOH A2199 HOH A2200 HOH A2201
SITE 1 AC5 15 GLY B 19 SER B 20 THR B 21 GLY B 22
SITE 2 AC5 15 SER B 23 ALA B 46 GLY B 47 GLY B 48
SITE 3 AC5 15 ALA B 49 HIS B 50 ALA B 69 ALA B 103
SITE 4 AC5 15 LEU B 104 VAL B 105 LEU B 108
CRYST1 67.614 65.323 86.179 90.00 101.89 90.00 P 1 21 1 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 0.014790 0.000000 0.003114 0.00000
SCALE2 0.000000 0.015309 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011858 0.00000
MTRIX1 1 -0.487500 0.860200 0.149700 39.10180 1
MTRIX2 1 0.849900 0.428400 0.306800 -12.92900 1
MTRIX3 1 0.199800 0.276800 -0.939900 -49.00490 1
(ATOM LINES ARE NOT SHOWN.)
END
