HEADER OXIDOREDUCTASE 02-MAR-09 3A06
TITLE CRYSTAL STRUCTURE OF DXR FROM THERMOOGA MARITIA, IN COMPLEX WITH
TITLE 2 FOSMIDOMYCIN AND NADPH
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: DXP REDUCTOISOMERASE, 1-DEOXYXYLULOSE-5-PHOSPHATE
COMPND 5 REDUCTOISOMERASE, 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE SYNTHASE;
COMPND 6 EC: 1.1.1.267;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA;
SOURCE 3 ORGANISM_TAXID: 2336;
SOURCE 4 STRAIN: MSB8;
SOURCE 5 GENE: DXR;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B (+)
KEYWDS REDUCTOISOMERASE, MEP PATHWAY, ISOPRENE BIOSYNTHESIS, METAL-BINDING,
KEYWDS 2 NADP, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.TAKENOYA,A.OHTAKI,K.NOGUCHI,Y.SASAKI,K.OHSAWA,M.YOHDA,S.YAJIMA
REVDAT 3 13-MAR-24 3A06 1 REMARK LINK
REVDAT 2 19-MAY-10 3A06 1 JRNL
REVDAT 1 16-MAR-10 3A06 0
JRNL AUTH M.TAKENOYA,A.OHTAKI,K.NOGUCHI,K.ENDO,Y.SASAKI,K.OHSAWA,
JRNL AUTH 2 S.YAJIMA,M.YOHDA
JRNL TITL CRYSTAL STRUCTURE OF 1-DEOXY-D-XYLULOSE 5-PHOSPHATE
JRNL TITL 2 REDUCTOISOMERASE FROM THE HYPERTHERMOPHILE THERMOTOGA
JRNL TITL 3 MARITIMA FOR INSIGHTS INTO THE COORDINATION OF
JRNL TITL 4 CONFORMATIONAL CHANGES AND AN INHIBITOR BINDING
JRNL REF J.STRUCT.BIOL. V. 170 532 2010
JRNL REFN ISSN 1047-8477
JRNL PMID 20353826
JRNL DOI 10.1016/J.JSB.2010.03.015
REMARK 2
REMARK 2 RESOLUTION. 2.00 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) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.72
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 55490
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) : 0.209
REMARK 3 R VALUE (WORKING SET) : 0.207
REMARK 3 FREE R VALUE : 0.240
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2953
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) : 2.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4104
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79
REMARK 3 BIN R VALUE (WORKING SET) : 0.2280
REMARK 3 BIN FREE R VALUE SET COUNT : 222
REMARK 3 BIN FREE R VALUE : 0.2690
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5872
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 135
REMARK 3 SOLVENT ATOMS : 113
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.39
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.10000
REMARK 3 B22 (A**2) : -0.10000
REMARK 3 B33 (A**2) : 0.19000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.188
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.025
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6143 ; 0.013 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8324 ; 1.472 ; 2.005
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 741 ; 5.635 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 256 ;36.332 ;23.828
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1112 ;16.931 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;17.530 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 958 ; 0.104 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4475 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2735 ; 0.215 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4212 ; 0.309 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 211 ; 0.244 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.088 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.244 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.143 ; 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): 3799 ; 1.060 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6016 ; 1.714 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2633 ; 2.596 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2308 ; 4.347 ; 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 RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3A06 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-MAR-09.
REMARK 100 THE DEPOSITION ID IS D_1000028645.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-APR-08
REMARK 200 TEMPERATURE (KELVIN) : 95
REMARK 200 PH : 5.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PHOTON FACTORY
REMARK 200 BEAMLINE : AR-NW12A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58356
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
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: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 52.80
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 35% MPD, PH 5.0, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y,X,Z+3/4
REMARK 290 4555 Y,-X,Z+1/4
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.33100
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.99650
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.66550
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: 7100 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 30310 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 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 1
REMARK 465 GLU A 2
REMARK 465 SER A 373
REMARK 465 THR A 374
REMARK 465 SER A 375
REMARK 465 TYR A 376
REMARK 465 MET B 1
REMARK 465 SER B 375
REMARK 465 TYR B 376
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 ND2 ASN A 205 OP1 FOM A 900 1.91
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 HIS A 37 -66.27 -103.39
REMARK 500 ASP A 65 -104.74 -147.49
REMARK 500 LYS A 186 -178.02 -170.41
REMARK 500 HIS A 187 -34.47 -133.75
REMARK 500 LEU A 270 -108.34 -112.88
REMARK 500 SER B 38 -14.16 -142.86
REMARK 500 ASP B 60 72.03 -105.07
REMARK 500 ASP B 65 -110.72 -118.70
REMARK 500 SER B 66 -45.08 -170.03
REMARK 500 GLU B 155 33.64 -99.31
REMARK 500 LEU B 185 46.30 -75.68
REMARK 500 VAL B 189 -38.34 -135.64
REMARK 500 MET B 203 18.09 59.91
REMARK 500 LEU B 270 -117.76 -117.35
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 3003
REMARK 610 FOM A 900
REMARK 610 FOM B 901
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 MG A 500 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 142 OD1
REMARK 620 2 GLU A 144 OE1 92.2
REMARK 620 3 GLU A 209 OE2 76.8 100.6
REMARK 620 4 HOH A 601 O 86.2 96.9 155.9
REMARK 620 5 HOH A 602 O 157.8 109.7 94.5 95.1
REMARK 620 6 HOH A 603 O 86.9 169.0 89.9 72.1 72.5
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG B 501 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 142 OD1
REMARK 620 2 GLU B 144 OE1 114.9
REMARK 620 3 GLU B 209 OE2 77.6 85.2
REMARK 620 4 HOH B 380 O 90.5 107.2 165.7
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 3001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 3003
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOM A 900
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 500
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 3002
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOM B 901
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 501
DBREF 3A06 A 1 376 UNP Q9WZZ1 DXR_THEMA 1 376
DBREF 3A06 B 1 376 UNP Q9WZZ1 DXR_THEMA 1 376
SEQRES 1 A 376 MET GLU GLU ARG THR LEU VAL ILE LEU GLY ALA THR GLY
SEQRES 2 A 376 SER ILE GLY THR GLN THR LEU ASP VAL LEU LYS LYS VAL
SEQRES 3 A 376 LYS GLY ILE ARG LEU ILE GLY ILE SER PHE HIS SER ASN
SEQRES 4 A 376 LEU GLU LEU ALA PHE LYS ILE VAL LYS GLU PHE ASN VAL
SEQRES 5 A 376 LYS ASN VAL ALA ILE THR GLY ASP VAL GLU PHE GLU ASP
SEQRES 6 A 376 SER SER ILE ASN VAL TRP LYS GLY SER HIS SER ILE GLU
SEQRES 7 A 376 GLU MET LEU GLU ALA LEU LYS PRO ASP ILE THR MET VAL
SEQRES 8 A 376 ALA VAL SER GLY PHE SER GLY LEU ARG ALA VAL LEU ALA
SEQRES 9 A 376 SER LEU GLU HIS SER LYS ARG VAL CYS LEU ALA ASN LYS
SEQRES 10 A 376 GLU SER LEU VAL CYS GLY GLY PHE LEU VAL LYS LYS LYS
SEQRES 11 A 376 LEU LYS GLU LYS GLY THR GLU LEU ILE PRO VAL ASP SER
SEQRES 12 A 376 GLU HIS SER ALA ILE PHE GLN VAL MET GLU PRO GLU VAL
SEQRES 13 A 376 GLU LYS VAL VAL LEU THR ALA SER GLY GLY ALA LEU ARG
SEQRES 14 A 376 ASP TRP LYS ILE SER LYS ILE ASP ARG ALA ARG PRO GLU
SEQRES 15 A 376 ASP VAL LEU LYS HIS PRO VAL TRP ASN MET GLY ALA ARG
SEQRES 16 A 376 ILE THR VAL ASP SER ALA THR MET VAL ASN LYS ALA PHE
SEQRES 17 A 376 GLU VAL LEU GLU ALA MET GLU LEU PHE GLU LEU PRO PHE
SEQRES 18 A 376 GLU LYS ILE GLU VAL LYS ILE HIS ARG GLU GLY LEU VAL
SEQRES 19 A 376 HIS GLY ALA VAL VAL LEU PRO ASP GLY ASN VAL LYS MET
SEQRES 20 A 376 VAL VAL SER PRO PRO ASP MET ARG ILE PRO ILE SER TYR
SEQRES 21 A 376 ALA LEU PHE TYR PRO ARG ARG VAL ALA LEU GLU PRO PHE
SEQRES 22 A 376 PHE LEU ARG THR ILE SER LEU SER PHE GLU ASP PRO ASP
SEQRES 23 A 376 PRO GLU LYS TYR PRO ALA PHE PHE LEU LEU LYS GLU ILE
SEQRES 24 A 376 LYS ASP SER TYR ALA LEU ARG THR ALA PHE ASN ALA ALA
SEQRES 25 A 376 ASP GLU VAL ALA VAL GLU ALA PHE LEU LYS GLY ARG ILE
SEQRES 26 A 376 ARG PHE GLY GLY ILE HIS ARG VAL ILE GLU LYS THR LEU
SEQRES 27 A 376 GLU GLU PHE GLN GLY TYR PRO GLN PRO ARG THR LEU ASP
SEQRES 28 A 376 ASP VAL GLU ARG ILE HIS PHE GLU ALA ILE LYS LYS ALA
SEQRES 29 A 376 GLU ARG VAL THR GLU TRP LEU SER SER THR SER TYR
SEQRES 1 B 376 MET GLU GLU ARG THR LEU VAL ILE LEU GLY ALA THR GLY
SEQRES 2 B 376 SER ILE GLY THR GLN THR LEU ASP VAL LEU LYS LYS VAL
SEQRES 3 B 376 LYS GLY ILE ARG LEU ILE GLY ILE SER PHE HIS SER ASN
SEQRES 4 B 376 LEU GLU LEU ALA PHE LYS ILE VAL LYS GLU PHE ASN VAL
SEQRES 5 B 376 LYS ASN VAL ALA ILE THR GLY ASP VAL GLU PHE GLU ASP
SEQRES 6 B 376 SER SER ILE ASN VAL TRP LYS GLY SER HIS SER ILE GLU
SEQRES 7 B 376 GLU MET LEU GLU ALA LEU LYS PRO ASP ILE THR MET VAL
SEQRES 8 B 376 ALA VAL SER GLY PHE SER GLY LEU ARG ALA VAL LEU ALA
SEQRES 9 B 376 SER LEU GLU HIS SER LYS ARG VAL CYS LEU ALA ASN LYS
SEQRES 10 B 376 GLU SER LEU VAL CYS GLY GLY PHE LEU VAL LYS LYS LYS
SEQRES 11 B 376 LEU LYS GLU LYS GLY THR GLU LEU ILE PRO VAL ASP SER
SEQRES 12 B 376 GLU HIS SER ALA ILE PHE GLN VAL MET GLU PRO GLU VAL
SEQRES 13 B 376 GLU LYS VAL VAL LEU THR ALA SER GLY GLY ALA LEU ARG
SEQRES 14 B 376 ASP TRP LYS ILE SER LYS ILE ASP ARG ALA ARG PRO GLU
SEQRES 15 B 376 ASP VAL LEU LYS HIS PRO VAL TRP ASN MET GLY ALA ARG
SEQRES 16 B 376 ILE THR VAL ASP SER ALA THR MET VAL ASN LYS ALA PHE
SEQRES 17 B 376 GLU VAL LEU GLU ALA MET GLU LEU PHE GLU LEU PRO PHE
SEQRES 18 B 376 GLU LYS ILE GLU VAL LYS ILE HIS ARG GLU GLY LEU VAL
SEQRES 19 B 376 HIS GLY ALA VAL VAL LEU PRO ASP GLY ASN VAL LYS MET
SEQRES 20 B 376 VAL VAL SER PRO PRO ASP MET ARG ILE PRO ILE SER TYR
SEQRES 21 B 376 ALA LEU PHE TYR PRO ARG ARG VAL ALA LEU GLU PRO PHE
SEQRES 22 B 376 PHE LEU ARG THR ILE SER LEU SER PHE GLU ASP PRO ASP
SEQRES 23 B 376 PRO GLU LYS TYR PRO ALA PHE PHE LEU LEU LYS GLU ILE
SEQRES 24 B 376 LYS ASP SER TYR ALA LEU ARG THR ALA PHE ASN ALA ALA
SEQRES 25 B 376 ASP GLU VAL ALA VAL GLU ALA PHE LEU LYS GLY ARG ILE
SEQRES 26 B 376 ARG PHE GLY GLY ILE HIS ARG VAL ILE GLU LYS THR LEU
SEQRES 27 B 376 GLU GLU PHE GLN GLY TYR PRO GLN PRO ARG THR LEU ASP
SEQRES 28 B 376 ASP VAL GLU ARG ILE HIS PHE GLU ALA ILE LYS LYS ALA
SEQRES 29 B 376 GLU ARG VAL THR GLU TRP LEU SER SER THR SER TYR
HET NDP A3001 48
HET NDP A3003 27
HET FOM A 900 5
HET MG A 500 1
HET NDP B3002 48
HET FOM B 901 5
HET MG B 501 1
HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
HETNAM 2 NDP PHOSPHATE
HETNAM FOM 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID
HETNAM MG MAGNESIUM ION
HETSYN FOM FOSMIDOMYCIN
FORMUL 3 NDP 3(C21 H30 N7 O17 P3)
FORMUL 5 FOM 2(C4 H10 N O5 P)
FORMUL 6 MG 2(MG 2+)
FORMUL 10 HOH *113(H2 O)
HELIX 1 1 GLY A 13 VAL A 26 1 14
HELIX 2 2 ASN A 39 ASN A 51 1 13
HELIX 3 3 HIS A 75 LYS A 85 1 11
HELIX 4 4 SER A 97 SER A 109 1 13
HELIX 5 5 LYS A 117 GLY A 135 1 19
HELIX 6 6 ASP A 142 MET A 152 1 11
HELIX 7 7 LYS A 172 ASP A 177 1 6
HELIX 8 8 ARG A 180 VAL A 184 5 5
HELIX 9 9 GLY A 193 MET A 203 1 11
HELIX 10 10 MET A 203 GLU A 218 1 16
HELIX 11 11 PRO A 220 GLU A 222 5 3
HELIX 12 12 MET A 254 TYR A 264 1 11
HELIX 13 13 ALA A 292 PHE A 294 5 3
HELIX 14 14 LEU A 295 LYS A 300 1 6
HELIX 15 15 SER A 302 LYS A 322 1 21
HELIX 16 16 GLY A 328 GLU A 340 1 13
HELIX 17 17 THR A 349 SER A 372 1 24
HELIX 18 18 GLY B 13 LYS B 25 1 13
HELIX 19 19 ASN B 39 ASN B 51 1 13
HELIX 20 20 HIS B 75 LYS B 85 1 11
HELIX 21 21 SER B 97 SER B 109 1 13
HELIX 22 22 LYS B 117 GLY B 135 1 19
HELIX 23 23 ASP B 142 MET B 152 1 11
HELIX 24 24 LYS B 172 ASP B 177 1 6
HELIX 25 25 ARG B 180 LEU B 185 1 6
HELIX 26 26 GLY B 193 MET B 203 1 11
HELIX 27 27 MET B 203 GLU B 218 1 16
HELIX 28 28 PRO B 220 GLU B 222 5 3
HELIX 29 29 MET B 254 TYR B 264 1 11
HELIX 30 30 ALA B 292 PHE B 294 5 3
HELIX 31 31 LEU B 295 LYS B 300 1 6
HELIX 32 32 SER B 302 LYS B 322 1 21
HELIX 33 33 GLY B 328 GLU B 340 1 13
HELIX 34 34 THR B 349 THR B 374 1 26
SHEET 1 A 7 ASN A 69 LYS A 72 0
SHEET 2 A 7 ASN A 54 ILE A 57 1 N VAL A 55 O TRP A 71
SHEET 3 A 7 ILE A 29 PHE A 36 1 N ILE A 34 O ALA A 56
SHEET 4 A 7 ARG A 4 LEU A 9 1 N ARG A 4 O ARG A 30
SHEET 5 A 7 ILE A 88 VAL A 91 1 O MET A 90 N VAL A 7
SHEET 6 A 7 ARG A 111 LEU A 114 1 O CYS A 113 N THR A 89
SHEET 7 A 7 GLU A 137 PRO A 140 1 O ILE A 139 N VAL A 112
SHEET 1 B 8 ILE A 224 ILE A 228 0
SHEET 2 B 8 LYS A 158 ALA A 163 1 N VAL A 159 O GLU A 225
SHEET 3 B 8 VAL A 234 VAL A 239 -1 O ALA A 237 N VAL A 160
SHEET 4 B 8 VAL A 245 VAL A 249 -1 O LYS A 246 N VAL A 238
SHEET 5 B 8 VAL B 245 VAL B 249 -1 O VAL B 249 N VAL A 245
SHEET 6 B 8 VAL B 234 VAL B 239 -1 N VAL B 238 O LYS B 246
SHEET 7 B 8 LYS B 158 ALA B 163 -1 N LYS B 158 O VAL B 239
SHEET 8 B 8 ILE B 224 ILE B 228 1 O GLU B 225 N VAL B 159
SHEET 1 C 2 ILE A 278 LEU A 280 0
SHEET 2 C 2 ILE B 278 LEU B 280 -1 O ILE B 278 N LEU A 280
SHEET 1 D 7 ASN B 69 TRP B 71 0
SHEET 2 D 7 ASN B 54 ILE B 57 1 N VAL B 55 O TRP B 71
SHEET 3 D 7 ILE B 29 PHE B 36 1 N ILE B 34 O ALA B 56
SHEET 4 D 7 ARG B 4 LEU B 9 1 N ARG B 4 O ARG B 30
SHEET 5 D 7 ILE B 88 VAL B 91 1 O MET B 90 N LEU B 9
SHEET 6 D 7 ARG B 111 LEU B 114 1 O CYS B 113 N VAL B 91
SHEET 7 D 7 GLU B 137 PRO B 140 1 O GLU B 137 N VAL B 112
LINK OD1 ASP A 142 MG MG A 500 1555 1555 2.16
LINK OE1BGLU A 144 MG MG A 500 1555 1555 1.89
LINK OE2 GLU A 209 MG MG A 500 1555 1555 2.18
LINK MG MG A 500 O HOH A 601 1555 1555 2.60
LINK MG MG A 500 O HOH A 602 1555 1555 2.28
LINK MG MG A 500 O HOH A 603 1555 1555 2.07
LINK OD1 ASP B 142 MG MG B 501 1555 1555 2.14
LINK OE1 GLU B 144 MG MG B 501 1555 1555 2.02
LINK OE2 GLU B 209 MG MG B 501 1555 1555 1.92
LINK O HOH B 380 MG MG B 501 1555 1555 2.41
CISPEP 1 GLU A 64 ASP A 65 0 -19.62
CISPEP 2 ASP A 65 SER A 66 0 -15.41
CISPEP 3 LEU A 185 LYS A 186 0 -1.22
CISPEP 4 LYS A 186 HIS A 187 0 -14.47
CISPEP 5 HIS A 187 PRO A 188 0 -9.06
CISPEP 6 TYR A 264 PRO A 265 0 5.40
CISPEP 7 GLU B 64 ASP B 65 0 -17.91
CISPEP 8 ASP B 65 SER B 66 0 1.34
CISPEP 9 TYR B 264 PRO B 265 0 3.40
SITE 1 AC1 24 GLY A 10 THR A 12 GLY A 13 SER A 14
SITE 2 AC1 24 ILE A 15 HIS A 37 SER A 38 ASN A 39
SITE 3 AC1 24 THR A 58 ALA A 92 VAL A 93 SER A 94
SITE 4 AC1 24 SER A 97 ALA A 115 ASN A 116 LYS A 117
SITE 5 AC1 24 GLU A 118 MET A 192 ILE A 196 HOH A 378
SITE 6 AC1 24 HOH A 380 HOH A 414 HOH A 420 HOH A 603
SITE 1 AC2 9 LYS A 24 ILE A 29 ARG A 30 LEU A 31
SITE 2 AC2 9 PHE A 50 HOH A 393 LYS B 45 LYS B 48
SITE 3 AC2 9 HOH B 412
SITE 1 AC3 9 GLU A 144 ALA A 163 SER A 164 TRP A 190
SITE 2 AC3 9 SER A 200 ASN A 205 LYS A 206 HOH A 431
SITE 3 AC3 9 HOH A 602
SITE 1 AC4 6 ASP A 142 GLU A 144 GLU A 209 HOH A 601
SITE 2 AC4 6 HOH A 602 HOH A 603
SITE 1 AC5 23 GLY B 10 THR B 12 GLY B 13 SER B 14
SITE 2 AC5 23 ILE B 15 HIS B 37 SER B 38 ASN B 39
SITE 3 AC5 23 THR B 58 ALA B 92 VAL B 93 SER B 94
SITE 4 AC5 23 SER B 97 ALA B 115 ASN B 116 LYS B 117
SITE 5 AC5 23 GLU B 118 ASP B 142 ILE B 196 MET B 254
SITE 6 AC5 23 HOH B 385 HOH B 407 HOH B 424
SITE 1 AC6 7 ALA B 163 SER B 164 TRP B 190 SER B 200
SITE 2 AC6 7 ASN B 205 LYS B 206 HOH B 440
SITE 1 AC7 4 ASP B 142 GLU B 144 GLU B 209 HOH B 380
CRYST1 108.622 108.622 74.662 90.00 90.00 90.00 P 43 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 0.009206 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009206 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013394 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
