HEADER OXIDOREDUCTASE 03-SEP-10 3ANL
TITLE CRYSTAL STRUCTURE OF 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
TITLE 2 (DXR) COMPLEXED WITH PYRIDIN-2-YLMETHYLPHOSPHONIC ACID
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: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 83333;
SOURCE 4 STRAIN: K12;
SOURCE 5 GENE: DXR, ISPC, YAEM, B0173, JW0168;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE30
KEYWDS REDUCTOISOMERASE, NADPH BINDING, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR K.ENDO,M.KATO,L.DENG,Y.SONG,S.YAJIMA
REVDAT 3 01-NOV-23 3ANL 1 REMARK SEQADV
REVDAT 2 19-OCT-11 3ANL 1 JRNL VERSN
REVDAT 1 23-FEB-11 3ANL 0
JRNL AUTH L.DENG,K.ENDO,M.KATO,G.CHENG,S.YAJIMA,Y.SONG
JRNL TITL STRUCTURES OF 1-DEOXY-D-XYLULOSE-5-PHOSPHATE
JRNL TITL 2 REDUCTOISOMERASE/LIPOPHILIC PHOSPHONATE COMPLEXES
JRNL REF ACS MED CHEM LETT V. 2 165 2011
JRNL REFN ISSN 1948-5875
JRNL PMID 21379374
JRNL DOI 10.1021/ML100243R
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) : 29.20
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 3 NUMBER OF REFLECTIONS : 52715
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) : 0.186
REMARK 3 R VALUE (WORKING SET) : 0.184
REMARK 3 FREE R VALUE : 0.225
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2822
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) : 2.16
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3825
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.09
REMARK 3 BIN R VALUE (WORKING SET) : 0.1990
REMARK 3 BIN FREE R VALUE SET COUNT : 201
REMARK 3 BIN FREE R VALUE : 0.2610
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6061
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 118
REMARK 3 SOLVENT ATOMS : 413
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.83
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.59000
REMARK 3 B22 (A**2) : 0.58000
REMARK 3 B33 (A**2) : -1.17000
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): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.171
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.995
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6285 ; 0.018 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8541 ; 1.804 ; 1.991
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 796 ; 5.588 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 262 ;42.025 ;24.656
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1073 ;15.691 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;20.848 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 994 ; 0.141 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4664 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3173 ; 0.219 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4345 ; 0.301 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 456 ; 0.161 ; 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): 40 ; 0.213 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.134 ; 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): 4106 ; 1.128 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6395 ; 1.842 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2441 ; 3.016 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2146 ; 4.687 ; 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 3ANL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-SEP-10.
REMARK 100 THE DEPOSITION ID IS D_1000029469.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-MAR-10
REMARK 200 TEMPERATURE (KELVIN) : 95
REMARK 200 PH : 5.6
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 : NUMERICAL LINK TYPE SI(111)
REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR
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 : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55758
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 3.500
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) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3
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: 2EGH
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 52.07
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE, 0.8M SODIUM
REMARK 280 MALONATE, 0.3M POTASSIUM SODIUM (+) TARTRATE, 3MM NADPH, 5MM
REMARK 280 MGCL2, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X+1/2,Y+1/2,-Z
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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 90.85850
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.64900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 90.85850
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.64900
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: 3200 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 31540 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 -10
REMARK 465 ARG A -9
REMARK 465 GLY A -8
REMARK 465 SER 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 HIS A -1
REMARK 465 CYS A 400
REMARK 465 ASP A 401
REMARK 465 LEU A 402
REMARK 465 GLY A 403
REMARK 465 THR A 404
REMARK 465 PRO A 405
REMARK 465 GLY A 406
REMARK 465 ARG A 407
REMARK 465 PRO A 408
REMARK 465 ALA A 409
REMARK 465 MET B -10
REMARK 465 ARG B -9
REMARK 465 GLY B -8
REMARK 465 SER B -7
REMARK 465 HIS 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 SER B 398
REMARK 465 ALA B 399
REMARK 465 CYS B 400
REMARK 465 ASP B 401
REMARK 465 LEU B 402
REMARK 465 GLY B 403
REMARK 465 THR B 404
REMARK 465 PRO B 405
REMARK 465 GLY B 406
REMARK 465 ARG B 407
REMARK 465 PRO B 408
REMARK 465 ALA B 409
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 C ALA B 122 O HOH B 410 1.91
REMARK 500 NE ARG B 288 O HOH B 412 1.99
REMARK 500 N ASN B 123 O HOH B 410 2.04
REMARK 500 O ALA B 122 O4D NDP B 702 2.08
REMARK 500 OE1 GLU B 272 O HOH B 465 2.10
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 3 CA - CB - CG ANGL. DEV. = 15.1 DEGREES
REMARK 500 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 ARG B 21 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES
REMARK 500 ARG B 235 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 ARG B 235 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES
REMARK 500 LEU B 237 CA - CB - CG ANGL. DEV. = 17.0 DEGREES
REMARK 500 ARG B 288 NE - CZ - NH2 ANGL. DEV. = -3.6 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 GLN A 71 2.89 -62.20
REMARK 500 ARG A 207 74.39 -102.66
REMARK 500 SER A 257 174.05 164.80
REMARK 500 ASP A 367 73.15 -157.28
REMARK 500 SER A 398 -89.19 -138.21
REMARK 500 TRP B 211 -78.31 -151.66
REMARK 500 SER B 212 98.62 67.35
REMARK 500 SER B 257 174.12 166.94
REMARK 500 ASP B 274 114.14 -162.37
REMARK 500 ASP B 367 82.18 27.48
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SYC A 800
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 702
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SYC B 801
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2EGH RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH FOSMIDOMYCIN.
REMARK 900 RELATED ID: 1T1R RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH A BISPHOSPHONATE COMPOUND.
REMARK 900 RELATED ID: 1T1S RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH A BISPHOSPHONATE COMPOUND.
REMARK 900 RELATED ID: 1JVS RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH A SULFATE ION.
REMARK 900 RELATED ID: 3ANM RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH LIPOPHILIC PHOSPHONATE COMPOUNDS
REMARK 900 RELATED ID: 3ANN RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH LIPOPHILIC PHOSPHONATE COMPOUNDS
DBREF 3ANL A 1 397 UNP P45568 DXR_ECOLI 2 398
DBREF 3ANL B 1 397 UNP P45568 DXR_ECOLI 2 398
SEQADV 3ANL MET A -10 UNP P45568 EXPRESSION TAG
SEQADV 3ANL ARG A -9 UNP P45568 EXPRESSION TAG
SEQADV 3ANL GLY A -8 UNP P45568 EXPRESSION TAG
SEQADV 3ANL SER A -7 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS A -6 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS A -5 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS A -4 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS A -3 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS A -2 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS A -1 UNP P45568 EXPRESSION TAG
SEQADV 3ANL GLY A 0 UNP P45568 EXPRESSION TAG
SEQADV 3ANL SER A 398 UNP P45568 EXPRESSION TAG
SEQADV 3ANL ALA A 399 UNP P45568 EXPRESSION TAG
SEQADV 3ANL CYS A 400 UNP P45568 EXPRESSION TAG
SEQADV 3ANL ASP A 401 UNP P45568 EXPRESSION TAG
SEQADV 3ANL LEU A 402 UNP P45568 EXPRESSION TAG
SEQADV 3ANL GLY A 403 UNP P45568 EXPRESSION TAG
SEQADV 3ANL THR A 404 UNP P45568 EXPRESSION TAG
SEQADV 3ANL PRO A 405 UNP P45568 EXPRESSION TAG
SEQADV 3ANL GLY A 406 UNP P45568 EXPRESSION TAG
SEQADV 3ANL ARG A 407 UNP P45568 EXPRESSION TAG
SEQADV 3ANL PRO A 408 UNP P45568 EXPRESSION TAG
SEQADV 3ANL ALA A 409 UNP P45568 EXPRESSION TAG
SEQADV 3ANL MET B -10 UNP P45568 EXPRESSION TAG
SEQADV 3ANL ARG B -9 UNP P45568 EXPRESSION TAG
SEQADV 3ANL GLY B -8 UNP P45568 EXPRESSION TAG
SEQADV 3ANL SER B -7 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS B -6 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS B -5 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS B -4 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS B -3 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS B -2 UNP P45568 EXPRESSION TAG
SEQADV 3ANL HIS B -1 UNP P45568 EXPRESSION TAG
SEQADV 3ANL GLY B 0 UNP P45568 EXPRESSION TAG
SEQADV 3ANL SER B 398 UNP P45568 EXPRESSION TAG
SEQADV 3ANL ALA B 399 UNP P45568 EXPRESSION TAG
SEQADV 3ANL CYS B 400 UNP P45568 EXPRESSION TAG
SEQADV 3ANL ASP B 401 UNP P45568 EXPRESSION TAG
SEQADV 3ANL LEU B 402 UNP P45568 EXPRESSION TAG
SEQADV 3ANL GLY B 403 UNP P45568 EXPRESSION TAG
SEQADV 3ANL THR B 404 UNP P45568 EXPRESSION TAG
SEQADV 3ANL PRO B 405 UNP P45568 EXPRESSION TAG
SEQADV 3ANL GLY B 406 UNP P45568 EXPRESSION TAG
SEQADV 3ANL ARG B 407 UNP P45568 EXPRESSION TAG
SEQADV 3ANL PRO B 408 UNP P45568 EXPRESSION TAG
SEQADV 3ANL ALA B 409 UNP P45568 EXPRESSION TAG
SEQRES 1 A 420 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY LYS GLN
SEQRES 2 A 420 LEU THR ILE LEU GLY SER THR GLY SER ILE GLY CYS SER
SEQRES 3 A 420 THR LEU ASP VAL VAL ARG HIS ASN PRO GLU HIS PHE ARG
SEQRES 4 A 420 VAL VAL ALA LEU VAL ALA GLY LYS ASN VAL THR ARG MET
SEQRES 5 A 420 VAL GLU GLN CYS LEU GLU PHE SER PRO ARG TYR ALA VAL
SEQRES 6 A 420 MET ASP ASP GLU ALA SER ALA LYS LEU LEU LYS THR MET
SEQRES 7 A 420 LEU GLN GLN GLN GLY SER ARG THR GLU VAL LEU SER GLY
SEQRES 8 A 420 GLN GLN ALA ALA CYS ASP MET ALA ALA LEU GLU ASP VAL
SEQRES 9 A 420 ASP GLN VAL MET ALA ALA ILE VAL GLY ALA ALA GLY LEU
SEQRES 10 A 420 LEU PRO THR LEU ALA ALA ILE ARG ALA GLY LYS THR ILE
SEQRES 11 A 420 LEU LEU ALA ASN LYS GLU SER LEU VAL THR CYS GLY ARG
SEQRES 12 A 420 LEU PHE MET ASP ALA VAL LYS GLN SER LYS ALA GLN LEU
SEQRES 13 A 420 LEU PRO VAL ASP SER GLU HIS ASN ALA ILE PHE GLN SER
SEQRES 14 A 420 LEU PRO GLN PRO ILE GLN HIS ASN LEU GLY TYR ALA ASP
SEQRES 15 A 420 LEU GLU GLN ASN GLY VAL VAL SER ILE LEU LEU THR GLY
SEQRES 16 A 420 SER GLY GLY PRO PHE ARG GLU THR PRO LEU ARG ASP LEU
SEQRES 17 A 420 ALA THR MET THR PRO ASP GLN ALA CYS ARG HIS PRO ASN
SEQRES 18 A 420 TRP SER MET GLY ARG LYS ILE SER VAL ASP SER ALA THR
SEQRES 19 A 420 MET MET ASN LYS GLY LEU GLU TYR ILE GLU ALA ARG TRP
SEQRES 20 A 420 LEU PHE ASN ALA SER ALA SER GLN MET GLU VAL LEU ILE
SEQRES 21 A 420 HIS PRO GLN SER VAL ILE HIS SER MET VAL ARG TYR GLN
SEQRES 22 A 420 ASP GLY SER VAL LEU ALA GLN LEU GLY GLU PRO ASP MET
SEQRES 23 A 420 ARG THR PRO ILE ALA HIS THR MET ALA TRP PRO ASN ARG
SEQRES 24 A 420 VAL ASN SER GLY VAL LYS PRO LEU ASP PHE CYS LYS LEU
SEQRES 25 A 420 SER ALA LEU THR PHE ALA ALA PRO ASP TYR ASP ARG TYR
SEQRES 26 A 420 PRO CYS LEU LYS LEU ALA MET GLU ALA PHE GLU GLN GLY
SEQRES 27 A 420 GLN ALA ALA THR THR ALA LEU ASN ALA ALA ASN GLU ILE
SEQRES 28 A 420 THR VAL ALA ALA PHE LEU ALA GLN GLN ILE ARG PHE THR
SEQRES 29 A 420 ASP ILE ALA ALA LEU ASN LEU SER VAL LEU GLU LYS MET
SEQRES 30 A 420 ASP MET ARG GLU PRO GLN CYS VAL ASP ASP VAL LEU SER
SEQRES 31 A 420 VAL ASP ALA ASN ALA ARG GLU VAL ALA ARG LYS GLU VAL
SEQRES 32 A 420 MET ARG LEU ALA SER SER ALA CYS ASP LEU GLY THR PRO
SEQRES 33 A 420 GLY ARG PRO ALA
SEQRES 1 B 420 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY LYS GLN
SEQRES 2 B 420 LEU THR ILE LEU GLY SER THR GLY SER ILE GLY CYS SER
SEQRES 3 B 420 THR LEU ASP VAL VAL ARG HIS ASN PRO GLU HIS PHE ARG
SEQRES 4 B 420 VAL VAL ALA LEU VAL ALA GLY LYS ASN VAL THR ARG MET
SEQRES 5 B 420 VAL GLU GLN CYS LEU GLU PHE SER PRO ARG TYR ALA VAL
SEQRES 6 B 420 MET ASP ASP GLU ALA SER ALA LYS LEU LEU LYS THR MET
SEQRES 7 B 420 LEU GLN GLN GLN GLY SER ARG THR GLU VAL LEU SER GLY
SEQRES 8 B 420 GLN GLN ALA ALA CYS ASP MET ALA ALA LEU GLU ASP VAL
SEQRES 9 B 420 ASP GLN VAL MET ALA ALA ILE VAL GLY ALA ALA GLY LEU
SEQRES 10 B 420 LEU PRO THR LEU ALA ALA ILE ARG ALA GLY LYS THR ILE
SEQRES 11 B 420 LEU LEU ALA ASN LYS GLU SER LEU VAL THR CYS GLY ARG
SEQRES 12 B 420 LEU PHE MET ASP ALA VAL LYS GLN SER LYS ALA GLN LEU
SEQRES 13 B 420 LEU PRO VAL ASP SER GLU HIS ASN ALA ILE PHE GLN SER
SEQRES 14 B 420 LEU PRO GLN PRO ILE GLN HIS ASN LEU GLY TYR ALA ASP
SEQRES 15 B 420 LEU GLU GLN ASN GLY VAL VAL SER ILE LEU LEU THR GLY
SEQRES 16 B 420 SER GLY GLY PRO PHE ARG GLU THR PRO LEU ARG ASP LEU
SEQRES 17 B 420 ALA THR MET THR PRO ASP GLN ALA CYS ARG HIS PRO ASN
SEQRES 18 B 420 TRP SER MET GLY ARG LYS ILE SER VAL ASP SER ALA THR
SEQRES 19 B 420 MET MET ASN LYS GLY LEU GLU TYR ILE GLU ALA ARG TRP
SEQRES 20 B 420 LEU PHE ASN ALA SER ALA SER GLN MET GLU VAL LEU ILE
SEQRES 21 B 420 HIS PRO GLN SER VAL ILE HIS SER MET VAL ARG TYR GLN
SEQRES 22 B 420 ASP GLY SER VAL LEU ALA GLN LEU GLY GLU PRO ASP MET
SEQRES 23 B 420 ARG THR PRO ILE ALA HIS THR MET ALA TRP PRO ASN ARG
SEQRES 24 B 420 VAL ASN SER GLY VAL LYS PRO LEU ASP PHE CYS LYS LEU
SEQRES 25 B 420 SER ALA LEU THR PHE ALA ALA PRO ASP TYR ASP ARG TYR
SEQRES 26 B 420 PRO CYS LEU LYS LEU ALA MET GLU ALA PHE GLU GLN GLY
SEQRES 27 B 420 GLN ALA ALA THR THR ALA LEU ASN ALA ALA ASN GLU ILE
SEQRES 28 B 420 THR VAL ALA ALA PHE LEU ALA GLN GLN ILE ARG PHE THR
SEQRES 29 B 420 ASP ILE ALA ALA LEU ASN LEU SER VAL LEU GLU LYS MET
SEQRES 30 B 420 ASP MET ARG GLU PRO GLN CYS VAL ASP ASP VAL LEU SER
SEQRES 31 B 420 VAL ASP ALA ASN ALA ARG GLU VAL ALA ARG LYS GLU VAL
SEQRES 32 B 420 MET ARG LEU ALA SER SER ALA CYS ASP LEU GLY THR PRO
SEQRES 33 B 420 GLY ARG PRO ALA
HET NDP A 701 48
HET SYC A 800 11
HET NDP B 702 48
HET SYC B 801 11
HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
HETNAM 2 NDP PHOSPHATE
HETNAM SYC (PYRIDIN-2-YLMETHYL)PHOSPHONIC ACID
FORMUL 3 NDP 2(C21 H30 N7 O17 P3)
FORMUL 4 SYC 2(C6 H8 N O3 P)
FORMUL 7 HOH *413(H2 O)
HELIX 1 1 GLY A 10 ASN A 23 1 14
HELIX 2 2 ASN A 37 SER A 49 1 13
HELIX 3 3 ASP A 57 GLN A 71 1 15
HELIX 4 4 GLY A 80 ALA A 89 1 10
HELIX 5 5 GLY A 102 ALA A 104 5 3
HELIX 6 6 GLY A 105 ALA A 115 1 11
HELIX 7 7 LYS A 124 LYS A 142 1 19
HELIX 8 8 ASP A 149 SER A 158 1 10
HELIX 9 9 PRO A 160 HIS A 165 1 6
HELIX 10 10 LEU A 172 ASN A 175 5 4
HELIX 11 11 PRO A 193 MET A 200 5 8
HELIX 12 12 THR A 201 CYS A 206 1 6
HELIX 13 13 GLY A 214 THR A 223 1 10
HELIX 14 14 MET A 224 ASN A 239 1 16
HELIX 15 15 SER A 241 SER A 243 5 3
HELIX 16 16 MET A 275 TRP A 285 1 11
HELIX 17 17 ASP A 297 LEU A 301 5 5
HELIX 18 18 TYR A 314 GLY A 327 1 14
HELIX 19 19 GLY A 327 ALA A 347 1 21
HELIX 20 20 THR A 353 MET A 366 1 14
HELIX 21 21 CYS A 373 SER A 398 1 26
HELIX 22 22 GLY B 10 ASN B 23 1 14
HELIX 23 23 ASN B 37 SER B 49 1 13
HELIX 24 24 ASP B 57 GLN B 71 1 15
HELIX 25 25 GLY B 80 ALA B 89 1 10
HELIX 26 26 GLY B 102 ALA B 104 5 3
HELIX 27 27 GLY B 105 ALA B 115 1 11
HELIX 28 28 LYS B 124 LYS B 142 1 19
HELIX 29 29 ASP B 149 SER B 158 1 10
HELIX 30 30 PRO B 160 HIS B 165 1 6
HELIX 31 31 LEU B 172 ASN B 175 5 4
HELIX 32 32 PRO B 193 MET B 200 5 8
HELIX 33 33 THR B 201 CYS B 206 1 6
HELIX 34 34 GLY B 214 THR B 223 1 10
HELIX 35 35 MET B 224 ASN B 239 1 16
HELIX 36 36 SER B 241 SER B 243 5 3
HELIX 37 37 MET B 275 TRP B 285 1 11
HELIX 38 38 ASP B 297 LEU B 301 5 5
HELIX 39 39 TYR B 314 GLY B 327 1 14
HELIX 40 40 GLY B 327 ALA B 347 1 21
HELIX 41 41 THR B 353 ASP B 367 1 15
HELIX 42 42 CYS B 373 SER B 397 1 25
SHEET 1 A 7 GLU A 76 SER A 79 0
SHEET 2 A 7 TYR A 52 MET A 55 1 N ALA A 53 O LEU A 78
SHEET 3 A 7 PHE A 27 ALA A 34 1 N LEU A 32 O VAL A 54
SHEET 4 A 7 LYS A 1 LEU A 6 1 N LYS A 1 O ARG A 28
SHEET 5 A 7 GLN A 95 ALA A 98 1 O MET A 97 N LEU A 6
SHEET 6 A 7 THR A 118 LEU A 121 1 O LEU A 120 N ALA A 98
SHEET 7 A 7 GLN A 144 PRO A 147 1 O GLN A 144 N ILE A 119
SHEET 1 B 8 MET A 245 ILE A 249 0
SHEET 2 B 8 VAL A 177 GLY A 184 1 N LEU A 182 O GLU A 246
SHEET 3 B 8 ILE A 255 TYR A 261 -1 O MET A 258 N LEU A 181
SHEET 4 B 8 VAL A 266 LEU A 270 -1 O GLN A 269 N HIS A 256
SHEET 5 B 8 VAL B 266 LEU B 270 -1 O VAL B 266 N LEU A 270
SHEET 6 B 8 ILE B 255 TYR B 261 -1 N HIS B 256 O GLN B 269
SHEET 7 B 8 VAL B 177 GLY B 184 -1 N LEU B 181 O MET B 258
SHEET 8 B 8 MET B 245 ILE B 249 1 O GLU B 246 N LEU B 182
SHEET 1 C 7 GLU B 76 SER B 79 0
SHEET 2 C 7 TYR B 52 MET B 55 1 N ALA B 53 O LEU B 78
SHEET 3 C 7 PHE B 27 ALA B 34 1 N ALA B 34 O VAL B 54
SHEET 4 C 7 LYS B 1 LEU B 6 1 N LYS B 1 O ARG B 28
SHEET 5 C 7 GLN B 95 ALA B 98 1 O MET B 97 N LEU B 6
SHEET 6 C 7 THR B 118 LEU B 121 1 O LEU B 120 N ALA B 98
SHEET 7 C 7 GLN B 144 PRO B 147 1 O GLN B 144 N ILE B 119
CISPEP 1 TRP A 285 PRO A 286 0 8.05
CISPEP 2 TRP B 285 PRO B 286 0 6.68
SITE 1 AC1 24 GLY A 7 THR A 9 GLY A 10 SER A 11
SITE 2 AC1 24 ILE A 12 ALA A 34 GLY A 35 LYS A 36
SITE 3 AC1 24 ASN A 37 ASP A 56 ALA A 99 ILE A 100
SITE 4 AC1 24 VAL A 101 ALA A 104 ALA A 122 ASN A 123
SITE 5 AC1 24 LYS A 124 ASP A 149 MET A 275 HOH A 449
SITE 6 AC1 24 HOH A 473 HOH A 491 HOH A 541 HOH A 594
SITE 1 AC2 12 GLY A 184 SER A 185 HIS A 208 ASN A 210
SITE 2 AC2 12 TRP A 211 SER A 221 ASN A 226 LYS A 227
SITE 3 AC2 12 SER A 253 HOH A 419 HOH A 427 HOH A 448
SITE 1 AC3 23 GLY B 7 THR B 9 GLY B 10 SER B 11
SITE 2 AC3 23 ILE B 12 ALA B 34 GLY B 35 LYS B 36
SITE 3 AC3 23 ASN B 37 ASP B 56 ALA B 99 ILE B 100
SITE 4 AC3 23 VAL B 101 ALA B 104 ALA B 122 ASN B 123
SITE 5 AC3 23 LYS B 124 ASP B 149 MET B 275 HOH B 442
SITE 6 AC3 23 HOH B 457 HOH B 467 HOH B 538
SITE 1 AC4 12 GLY B 184 SER B 185 HIS B 208 ASN B 210
SITE 2 AC4 12 TRP B 211 SER B 221 ASN B 226 LYS B 227
SITE 3 AC4 12 SER B 253 HOH B 422 HOH B 423 HOH B 446
CRYST1 181.717 59.298 87.166 90.00 90.00 90.00 P 21 21 2 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 0.005503 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016864 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011472 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
