HEADER OXIDOREDUCTASE 16-JUL-03 1Q0H
TITLE CRYSTAL STRUCTURE OF SELENOMETHIONINE-LABELLED DXR IN COMPLEX WITH
TITLE 2 FOSMIDOMYCIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: DXP REDUCTOISOMERASE, 1-DEOXYXYLULOSE-5-PHOSPHATE
COMPND 5 REDUCTOISOMERASE, ISPC;
COMPND 6 EC: 1.1.1.267;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 GENE: DXR;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDS-6HISNDEI
KEYWDS OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.MAC SWEENEY,R.LANGE,A.D'ARCY,A.DOUANGAMATH,J.-P.SURIVET,C.OEFNER
REVDAT 7 15-NOV-23 1Q0H 1 REMARK
REVDAT 6 16-AUG-23 1Q0H 1 REMARK SEQADV LINK
REVDAT 5 03-OCT-18 1Q0H 1 REMARK
REVDAT 4 13-JUL-11 1Q0H 1 VERSN
REVDAT 3 24-FEB-09 1Q0H 1 VERSN
REVDAT 2 01-MAR-05 1Q0H 1 JRNL
REVDAT 1 20-JUL-04 1Q0H 0
JRNL AUTH A.MAC SWEENEY,R.LANGE,R.P.FERNANDES,H.SCHULZ,G.E.DALE,
JRNL AUTH 2 A.DOUANGAMATH,P.J.PROTEAU,C.OEFNER
JRNL TITL THE CRYSTAL STRUCTURE OF E.COLI
JRNL TITL 2 1-DEOXY-D-XYLULOSE-5-PHOSPHATE REDUCTOISOMERASE IN A TERNARY
JRNL TITL 3 COMPLEX WITH THE ANTIMALARIAL COMPOUND FOSMIDOMYCIN AND
JRNL TITL 4 NADPH REVEALS A TIGHT-BINDING CLOSED ENZYME CONFORMATION.
JRNL REF J.MOL.BIOL. V. 345 115 2005
JRNL REFN ISSN 0022-2836
JRNL PMID 15567415
JRNL DOI 10.1016/J.JMB.2004.10.030
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.62
REMARK 3 DATA CUTOFF (SIGMA(F)) : 6.000
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 31219
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.189
REMARK 3 R VALUE (WORKING SET) : 0.187
REMARK 3 FREE R VALUE : 0.212
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 1580
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE SET COUNT : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3030
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 55
REMARK 3 SOLVENT ATOMS : 265
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 0.23
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.80
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
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): NULL
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 : NULL
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.010 ; NULL
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 1.175 ; NULL
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
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 : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : NULL
REMARK 3 ION PROBE RADIUS : NULL
REMARK 3 SHRINKAGE RADIUS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1Q0H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-03.
REMARK 100 THE DEPOSITION ID IS D_1000019761.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-MAR-03
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.0
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 : ENRAF-NONIUS FR571
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : OSMIC MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31221
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1
REMARK 200 DATA REDUNDANCY : 3.800
REMARK 200 R MERGE (I) : 0.12900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6400
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.46500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.970
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 1K5H (NADPH BINDING DOMAIN)
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 64.26
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.6M NACL, 0.1M ACETATE-HCL PH 5.0,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+2/3
REMARK 290 6555 -X,-X+Y,-Z+1/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.21000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.42000
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.42000
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.21000
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 300 REMARK: THE SECOND MOLECULE OF THE BIOLOGICAL HOMODIMER IS
REMARK 300 GENERATED BY THE TWO-FOLD AXIS. OPERATION X, Y, Z TO Y, X, 1-Z (NON-
REMARK 300 ORTHOGONAL COORDINATE SYSTEM)
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,PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 6220 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 30520 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL
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 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000
REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 90.63000
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 HIS A -7
REMARK 465 HIS A -6
REMARK 465 HIS A -5
REMARK 465 HIS A -4
REMARK 465 HIS A -3
REMARK 465 HIS A -2
REMARK 465 SER A -1
REMARK 465 GLY A 0
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 ARG A 29 CD NE CZ NH1 NH2
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 O HOH A 548 O HOH A 567 1.67
REMARK 500 O HOH A 545 O HOH A 564 2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 29 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 ASP A 58 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES
REMARK 500 ASP A 197 CB - CG - OD2 ANGL. DEV. = 5.5 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 SER A 258 174.72 171.60
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 NDP A 401
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOM A 400
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 402
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1Q0L RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF DXR IN COMPLEX WITH FOSMIDOMYCIN
REMARK 900 RELATED ID: 1Q0Q RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF DXR IN COMPLEX WITH THE SUBSTRATE 1-DEOXY-D-
REMARK 900 XYLULOSE-5-PHOSPHATE
DBREF 1Q0H A 1 398 UNP P45568 DXR_ECOLI 1 398
SEQADV 1Q0H HIS A -7 UNP P45568 EXPRESSION TAG
SEQADV 1Q0H HIS A -6 UNP P45568 EXPRESSION TAG
SEQADV 1Q0H HIS A -5 UNP P45568 EXPRESSION TAG
SEQADV 1Q0H HIS A -4 UNP P45568 EXPRESSION TAG
SEQADV 1Q0H HIS A -3 UNP P45568 EXPRESSION TAG
SEQADV 1Q0H HIS A -2 UNP P45568 EXPRESSION TAG
SEQADV 1Q0H SER A -1 UNP P45568 EXPRESSION TAG
SEQADV 1Q0H GLY A 0 UNP P45568 EXPRESSION TAG
SEQADV 1Q0H MSE A 1 UNP P45568 MET 1 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 42 UNP P45568 MET 42 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 56 UNP P45568 MET 56 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 68 UNP P45568 MET 68 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 88 UNP P45568 MET 88 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 98 UNP P45568 MET 98 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 136 UNP P45568 MET 136 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 201 UNP P45568 MET 201 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 214 UNP P45568 MET 214 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 225 UNP P45568 MET 225 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 226 UNP P45568 MET 226 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 246 UNP P45568 MET 246 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 259 UNP P45568 MET 259 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 276 UNP P45568 MET 276 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 284 UNP P45568 MET 284 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 322 UNP P45568 MET 322 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 367 UNP P45568 MET 367 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 369 UNP P45568 MET 369 MODIFIED RESIDUE
SEQADV 1Q0H MSE A 394 UNP P45568 MET 394 MODIFIED RESIDUE
SEQRES 1 A 406 HIS HIS HIS HIS HIS HIS SER GLY MSE LYS GLN LEU THR
SEQRES 2 A 406 ILE LEU GLY SER THR GLY SER ILE GLY CYS SER THR LEU
SEQRES 3 A 406 ASP VAL VAL ARG HIS ASN PRO GLU HIS PHE ARG VAL VAL
SEQRES 4 A 406 ALA LEU VAL ALA GLY LYS ASN VAL THR ARG MSE VAL GLU
SEQRES 5 A 406 GLN CYS LEU GLU PHE SER PRO ARG TYR ALA VAL MSE ASP
SEQRES 6 A 406 ASP GLU ALA SER ALA LYS LEU LEU LYS THR MSE LEU GLN
SEQRES 7 A 406 GLN GLN GLY SER ARG THR GLU VAL LEU SER GLY GLN GLN
SEQRES 8 A 406 ALA ALA CYS ASP MSE ALA ALA LEU GLU ASP VAL ASP GLN
SEQRES 9 A 406 VAL MSE ALA ALA ILE VAL GLY ALA ALA GLY LEU LEU PRO
SEQRES 10 A 406 THR LEU ALA ALA ILE ARG ALA GLY LYS THR ILE LEU LEU
SEQRES 11 A 406 ALA ASN LYS GLU SER LEU VAL THR CYS GLY ARG LEU PHE
SEQRES 12 A 406 MSE ASP ALA VAL LYS GLN SER LYS ALA GLN LEU LEU PRO
SEQRES 13 A 406 VAL ASP SER GLU HIS ASN ALA ILE PHE GLN SER LEU PRO
SEQRES 14 A 406 GLN PRO ILE GLN HIS ASN LEU GLY TYR ALA ASP LEU GLU
SEQRES 15 A 406 GLN ASN GLY VAL VAL SER ILE LEU LEU THR GLY SER GLY
SEQRES 16 A 406 GLY PRO PHE ARG GLU THR PRO LEU ARG ASP LEU ALA THR
SEQRES 17 A 406 MSE THR PRO ASP GLN ALA CYS ARG HIS PRO ASN TRP SER
SEQRES 18 A 406 MSE GLY ARG LYS ILE SER VAL ASP SER ALA THR MSE MSE
SEQRES 19 A 406 ASN LYS GLY LEU GLU TYR ILE GLU ALA ARG TRP LEU PHE
SEQRES 20 A 406 ASN ALA SER ALA SER GLN MSE GLU VAL LEU ILE HIS PRO
SEQRES 21 A 406 GLN SER VAL ILE HIS SER MSE VAL ARG TYR GLN ASP GLY
SEQRES 22 A 406 SER VAL LEU ALA GLN LEU GLY GLU PRO ASP MSE ARG THR
SEQRES 23 A 406 PRO ILE ALA HIS THR MSE ALA TRP PRO ASN ARG VAL ASN
SEQRES 24 A 406 SER GLY VAL LYS PRO LEU ASP PHE CYS LYS LEU SER ALA
SEQRES 25 A 406 LEU THR PHE ALA ALA PRO ASP TYR ASP ARG TYR PRO CYS
SEQRES 26 A 406 LEU LYS LEU ALA MSE GLU ALA PHE GLU GLN GLY GLN ALA
SEQRES 27 A 406 ALA THR THR ALA LEU ASN ALA ALA ASN GLU ILE THR VAL
SEQRES 28 A 406 ALA ALA PHE LEU ALA GLN GLN ILE ARG PHE THR ASP ILE
SEQRES 29 A 406 ALA ALA LEU ASN LEU SER VAL LEU GLU LYS MSE ASP MSE
SEQRES 30 A 406 ARG GLU PRO GLN CYS VAL ASP ASP VAL LEU SER VAL ASP
SEQRES 31 A 406 ALA ASN ALA ARG GLU VAL ALA ARG LYS GLU VAL MSE ARG
SEQRES 32 A 406 LEU ALA SER
MODRES 1Q0H MSE A 1 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 42 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 56 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 68 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 88 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 98 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 136 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 201 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 214 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 225 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 226 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 246 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 259 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 276 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 284 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 322 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 367 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 369 MET SELENOMETHIONINE
MODRES 1Q0H MSE A 394 MET SELENOMETHIONINE
HET MSE A 1 8
HET MSE A 42 8
HET MSE A 56 8
HET MSE A 68 8
HET MSE A 88 8
HET MSE A 98 8
HET MSE A 136 8
HET MSE A 201 8
HET MSE A 214 8
HET MSE A 225 8
HET MSE A 226 8
HET MSE A 246 8
HET MSE A 259 8
HET MSE A 276 8
HET MSE A 284 8
HET MSE A 322 8
HET MSE A 367 8
HET MSE A 369 8
HET MSE A 394 8
HET FOM A 400 11
HET NDP A 401 62
HET CIT A 402 13
HETNAM MSE SELENOMETHIONINE
HETNAM FOM 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID
HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
HETNAM 2 NDP PHOSPHATE
HETNAM CIT CITRIC ACID
HETSYN FOM FOSMIDOMYCIN
FORMUL 1 MSE 19(C5 H11 N O2 SE)
FORMUL 2 FOM C4 H10 N O5 P
FORMUL 3 NDP C21 H30 N7 O17 P3
FORMUL 4 CIT C6 H8 O7
FORMUL 5 HOH *265(H2 O)
HELIX 1 1 GLY A 11 ASN A 24 1 14
HELIX 2 2 ASN A 38 SER A 50 1 13
HELIX 3 3 ASP A 58 GLY A 73 1 16
HELIX 4 4 GLY A 81 ALA A 90 1 10
HELIX 5 5 GLY A 103 ALA A 105 5 3
HELIX 6 6 GLY A 106 ALA A 116 1 11
HELIX 7 7 ASN A 124 SER A 142 1 19
HELIX 8 8 ASP A 150 SER A 159 1 10
HELIX 9 9 PRO A 161 HIS A 166 1 6
HELIX 10 10 LEU A 173 ASN A 176 5 4
HELIX 11 11 PRO A 194 MSE A 201 5 8
HELIX 12 12 THR A 202 ARG A 208 1 7
HELIX 13 13 GLY A 215 THR A 224 1 10
HELIX 14 14 MSE A 225 PHE A 239 1 15
HELIX 15 15 SER A 242 SER A 244 5 3
HELIX 16 16 MSE A 276 TRP A 286 1 11
HELIX 17 17 ASP A 298 LEU A 302 5 5
HELIX 18 18 TYR A 315 GLY A 328 1 14
HELIX 19 19 GLY A 328 ALA A 348 1 21
HELIX 20 20 THR A 354 MSE A 367 1 14
HELIX 21 21 CYS A 374 LEU A 396 1 23
SHEET 1 A 7 GLU A 77 SER A 80 0
SHEET 2 A 7 TYR A 53 MSE A 56 1 N ALA A 54 O LEU A 79
SHEET 3 A 7 PHE A 28 ALA A 35 1 N ALA A 35 O VAL A 55
SHEET 4 A 7 LYS A 2 LEU A 7 1 N LEU A 4 O ARG A 29
SHEET 5 A 7 GLN A 96 ALA A 99 1 O MSE A 98 N LEU A 7
SHEET 6 A 7 THR A 119 LEU A 122 1 O LEU A 121 N ALA A 99
SHEET 7 A 7 LEU A 146 PRO A 148 1 O LEU A 147 N ILE A 120
SHEET 1 B 4 MSE A 246 ILE A 250 0
SHEET 2 B 4 VAL A 178 GLY A 185 1 N LEU A 183 O GLU A 247
SHEET 3 B 4 ILE A 256 TYR A 262 -1 O MSE A 259 N LEU A 182
SHEET 4 B 4 VAL A 267 LEU A 271 -1 O LEU A 268 N VAL A 260
LINK C MSE A 1 N LYS A 2 1555 1555 1.34
LINK C ARG A 41 N MSE A 42 1555 1555 1.33
LINK C MSE A 42 N VAL A 43 1555 1555 1.33
LINK C VAL A 55 N MSE A 56 1555 1555 1.33
LINK C MSE A 56 N ASP A 57 1555 1555 1.33
LINK C THR A 67 N MSE A 68 1555 1555 1.33
LINK C MSE A 68 N LEU A 69 1555 1555 1.33
LINK C ASP A 87 N MSE A 88 1555 1555 1.33
LINK C MSE A 88 N ALA A 89 1555 1555 1.33
LINK C VAL A 97 N MSE A 98 1555 1555 1.33
LINK C MSE A 98 N ALA A 99 1555 1555 1.33
LINK C PHE A 135 N MSE A 136 1555 1555 1.33
LINK C MSE A 136 N ASP A 137 1555 1555 1.33
LINK C THR A 200 N MSE A 201 1555 1555 1.33
LINK C MSE A 201 N THR A 202 1555 1555 1.33
LINK C SER A 213 N MSE A 214 1555 1555 1.33
LINK C MSE A 214 N GLY A 215 1555 1555 1.33
LINK C THR A 224 N MSE A 225 1555 1555 1.34
LINK C MSE A 225 N MSE A 226 1555 1555 1.33
LINK C MSE A 226 N ASN A 227 1555 1555 1.33
LINK C GLN A 245 N MSE A 246 1555 1555 1.33
LINK C MSE A 246 N GLU A 247 1555 1555 1.32
LINK C SER A 258 N MSE A 259 1555 1555 1.33
LINK C MSE A 259 N VAL A 260 1555 1555 1.34
LINK C ASP A 275 N MSE A 276 1555 1555 1.33
LINK C MSE A 276 N ARG A 277 1555 1555 1.33
LINK C THR A 283 N MSE A 284 1555 1555 1.33
LINK C MSE A 284 N ALA A 285 1555 1555 1.33
LINK C ALA A 321 N MSE A 322 1555 1555 1.33
LINK C MSE A 322 N GLU A 323 1555 1555 1.33
LINK C LYS A 366 N MSE A 367 1555 1555 1.33
LINK C MSE A 367 N ASP A 368 1555 1555 1.33
LINK C ASP A 368 N MSE A 369 1555 1555 1.33
LINK C MSE A 369 N ARG A 370 1555 1555 1.33
LINK C VAL A 393 N MSE A 394 1555 1555 1.33
LINK C MSE A 394 N ARG A 395 1555 1555 1.39
CISPEP 1 THR A 184 GLY A 185 0 -3.24
CISPEP 2 TRP A 286 PRO A 287 0 4.88
SITE 1 AC1 13 SER A 151 GLU A 152 GLY A 185 SER A 186
SITE 2 AC1 13 HIS A 209 SER A 222 ASN A 227 LYS A 228
SITE 3 AC1 13 GLU A 231 MSE A 276 HOH A 415 HOH A 464
SITE 4 AC1 13 HOH A 653
SITE 1 AC2 23 GLY A 8 THR A 10 GLY A 11 SER A 12
SITE 2 AC2 23 ILE A 13 ALA A 35 GLY A 36 LYS A 37
SITE 3 AC2 23 ASN A 38 ASP A 57 ILE A 101 VAL A 102
SITE 4 AC2 23 MSE A 214 GLY A 215 ARG A 216 LYS A 217
SITE 5 AC2 23 HOH A 413 HOH A 429 HOH A 559 HOH A 581
SITE 6 AC2 23 HOH A 587 HOH A 618 HOH A 647
SITE 1 AC3 7 CYS A 15 ARG A 41 ARG A 352 ALA A 397
SITE 2 AC3 7 SER A 398 HOH A 483 HOH A 629
CRYST1 109.168 109.168 90.630 90.00 90.00 120.00 P 31 2 1 6
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 0.009160 0.005289 0.000000 0.00000
SCALE2 0.000000 0.010577 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011034 0.00000
HETATM 1 N MSE A 1 28.502 5.611 48.629 1.00 39.40 N
HETATM 2 CA MSE A 1 29.628 6.391 48.030 1.00 39.56 C
HETATM 3 C MSE A 1 29.514 6.504 46.516 1.00 37.93 C
HETATM 4 O MSE A 1 29.096 5.557 45.858 1.00 38.01 O
HETATM 5 CB MSE A 1 30.967 5.738 48.352 1.00 40.53 C
HETATM 6 CG MSE A 1 32.140 6.678 48.091 1.00 44.35 C
HETATM 7 SE MSE A 1 33.831 6.145 48.879 1.00 54.73 SE
HETATM 8 CE MSE A 1 33.269 5.687 50.737 1.00 53.52 C
(ATOM LINES ARE NOT SHOWN.)
END
