HEADER OXIDOREDUCTASE 03-SEP-10 3ANN TITLE CRYSTAL STRUCTURE OF 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE TITLE 2 (DXR) COMPLEXED WITH QUINOLIN-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 3ANN 1 REMARK SEQADV REVDAT 2 19-OCT-11 3ANN 1 JRNL VERSN REVDAT 1 23-FEB-11 3ANN 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. 2.00 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) : 33.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 61556 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 : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3290 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) : 4492 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 245 REMARK 3 BIN FREE R VALUE : 0.2780 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 : 126 REMARK 3 SOLVENT ATOMS : 411 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.42000 REMARK 3 B22 (A**2) : 0.63000 REMARK 3 B33 (A**2) : -1.05000 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): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.296 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6295 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8557 ; 1.725 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 796 ; 7.689 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 262 ;41.788 ;24.656 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1073 ;16.302 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;19.279 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 994 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4672 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3163 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4356 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 426 ; 0.155 ; 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): 42 ; 0.183 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.106 ; 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): 4110 ; 1.041 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6395 ; 1.672 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2470 ; 2.881 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2162 ; 4.477 ; 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 3ANN 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_1000029471. 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 : 65518 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 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) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.0 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 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 (%): 52.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 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 91.31350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.63950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 91.31350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.63950 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: 3180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31590 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 O TRP B 211 O HOH B 486 1.98 REMARK 500 O ALA B 122 O4D NDP B 702 2.01 REMARK 500 NE ARG B 288 O HOH B 412 2.01 REMARK 500 NH2 ARG B 235 OE2 GLU B 325 2.15 REMARK 500 NH2 ARG B 288 O HOH B 412 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 288 CZ ARG B 288 NH1 0.084 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 A 159 CB - CG - CD1 ANGL. DEV. = 10.7 DEGREES REMARK 500 LEU B 3 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 21 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 235 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 235 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 LEU B 237 CA - CB - CG ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG B 288 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 288 NE - CZ - NH2 ANGL. DEV. = -6.7 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 210 30.46 -144.32 REMARK 500 SER A 257 173.44 161.18 REMARK 500 ASP A 367 57.88 -146.39 REMARK 500 SER A 398 -96.34 -129.96 REMARK 500 ASN B 210 35.36 -141.95 REMARK 500 TRP B 211 -59.56 -142.55 REMARK 500 SER B 257 172.71 169.43 REMARK 500 ASP B 367 84.41 10.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 208 PRO A 209 148.49 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 SYE 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 SYE 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: 3ANL RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH LIPOPHILIC PHOSPHONATE COMPOUNDS REMARK 900 RELATED ID: 3ANM RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH LIPOPHILIC PHOSPHONATE COMPOUNDS DBREF 3ANN A 1 397 UNP P45568 DXR_ECOLI 2 398 DBREF 3ANN B 1 397 UNP P45568 DXR_ECOLI 2 398 SEQADV 3ANN MET A -10 UNP P45568 EXPRESSION TAG SEQADV 3ANN ARG A -9 UNP P45568 EXPRESSION TAG SEQADV 3ANN GLY A -8 UNP P45568 EXPRESSION TAG SEQADV 3ANN SER A -7 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS A -6 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS A -5 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS A -4 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS A -3 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS A -2 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS A -1 UNP P45568 EXPRESSION TAG SEQADV 3ANN GLY A 0 UNP P45568 EXPRESSION TAG SEQADV 3ANN SER A 398 UNP P45568 EXPRESSION TAG SEQADV 3ANN ALA A 399 UNP P45568 EXPRESSION TAG SEQADV 3ANN CYS A 400 UNP P45568 EXPRESSION TAG SEQADV 3ANN ASP A 401 UNP P45568 EXPRESSION TAG SEQADV 3ANN LEU A 402 UNP P45568 EXPRESSION TAG SEQADV 3ANN GLY A 403 UNP P45568 EXPRESSION TAG SEQADV 3ANN THR A 404 UNP P45568 EXPRESSION TAG SEQADV 3ANN PRO A 405 UNP P45568 EXPRESSION TAG SEQADV 3ANN GLY A 406 UNP P45568 EXPRESSION TAG SEQADV 3ANN ARG A 407 UNP P45568 EXPRESSION TAG SEQADV 3ANN PRO A 408 UNP P45568 EXPRESSION TAG SEQADV 3ANN ALA A 409 UNP P45568 EXPRESSION TAG SEQADV 3ANN MET B -10 UNP P45568 EXPRESSION TAG SEQADV 3ANN ARG B -9 UNP P45568 EXPRESSION TAG SEQADV 3ANN GLY B -8 UNP P45568 EXPRESSION TAG SEQADV 3ANN SER B -7 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS B -6 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS B -5 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS B -4 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS B -3 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS B -2 UNP P45568 EXPRESSION TAG SEQADV 3ANN HIS B -1 UNP P45568 EXPRESSION TAG SEQADV 3ANN GLY B 0 UNP P45568 EXPRESSION TAG SEQADV 3ANN SER B 398 UNP P45568 EXPRESSION TAG SEQADV 3ANN ALA B 399 UNP P45568 EXPRESSION TAG SEQADV 3ANN CYS B 400 UNP P45568 EXPRESSION TAG SEQADV 3ANN ASP B 401 UNP P45568 EXPRESSION TAG SEQADV 3ANN LEU B 402 UNP P45568 EXPRESSION TAG SEQADV 3ANN GLY B 403 UNP P45568 EXPRESSION TAG SEQADV 3ANN THR B 404 UNP P45568 EXPRESSION TAG SEQADV 3ANN PRO B 405 UNP P45568 EXPRESSION TAG SEQADV 3ANN GLY B 406 UNP P45568 EXPRESSION TAG SEQADV 3ANN ARG B 407 UNP P45568 EXPRESSION TAG SEQADV 3ANN PRO B 408 UNP P45568 EXPRESSION TAG SEQADV 3ANN 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 SYE A 800 15 HET NDP B 702 48 HET SYE B 801 15 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM SYE (QUINOLIN-2-YLMETHYL)PHOSPHONIC ACID FORMUL 3 NDP 2(C21 H30 N7 O17 P3) FORMUL 4 SYE 2(C10 H10 N O3 P) FORMUL 7 HOH *411(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 THR B 129 1 6 HELIX 29 29 CYS B 130 LYS B 142 1 13 HELIX 30 30 ASP B 149 SER B 158 1 10 HELIX 31 31 PRO B 160 HIS B 165 1 6 HELIX 32 32 LEU B 172 ASN B 175 5 4 HELIX 33 33 PRO B 193 MET B 200 5 8 HELIX 34 34 THR B 201 CYS B 206 1 6 HELIX 35 35 GLY B 214 MET B 224 1 11 HELIX 36 36 MET B 224 ASN B 239 1 16 HELIX 37 37 SER B 241 SER B 243 5 3 HELIX 38 38 MET B 275 TRP B 285 1 11 HELIX 39 39 ASP B 297 LEU B 301 5 5 HELIX 40 40 TYR B 314 GLY B 327 1 14 HELIX 41 41 GLY B 327 ALA B 347 1 21 HELIX 42 42 THR B 353 ASP B 367 1 15 HELIX 43 43 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 LEU A 3 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 VAL A 96 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 ARG A 260 N VAL A 178 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 LEU B 270 N VAL A 266 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 8.04 CISPEP 2 TRP B 285 PRO B 286 0 4.74 SITE 1 AC1 23 GLY A 7 THR A 9 GLY A 10 SER A 11 SITE 2 AC1 23 ILE A 12 ALA A 34 GLY A 35 LYS A 36 SITE 3 AC1 23 ASN A 37 ASP A 56 ALA A 99 ILE A 100 SITE 4 AC1 23 VAL A 101 ALA A 104 ALA A 122 ASN A 123 SITE 5 AC1 23 LYS A 124 ASP A 149 MET A 275 HOH A 435 SITE 6 AC1 23 HOH A 444 HOH A 468 HOH A 485 SITE 1 AC2 14 GLY A 184 SER A 185 HIS A 208 ASN A 210 SITE 2 AC2 14 TRP A 211 SER A 221 ASN A 226 LYS A 227 SITE 3 AC2 14 SER A 253 PRO A 273 HOH A 415 HOH A 428 SITE 4 AC2 14 HOH A 429 HOH A 450 SITE 1 AC3 24 GLY B 7 THR B 9 GLY B 10 SER B 11 SITE 2 AC3 24 ILE B 12 ALA B 34 GLY B 35 LYS B 36 SITE 3 AC3 24 ASN B 37 ASP B 56 ALA B 99 ILE B 100 SITE 4 AC3 24 VAL B 101 ALA B 104 ALA B 122 ASN B 123 SITE 5 AC3 24 LYS B 124 ASP B 149 MET B 275 HOH B 428 SITE 6 AC3 24 HOH B 436 HOH B 463 HOH B 598 HOH B 603 SITE 1 AC4 14 GLY B 184 SER B 185 HIS B 208 ASN B 210 SITE 2 AC4 14 TRP B 211 SER B 221 ASN B 226 LYS B 227 SITE 3 AC4 14 SER B 253 PRO B 273 HOH B 411 HOH B 414 SITE 4 AC4 14 HOH B 426 HOH B 429 CRYST1 182.627 59.279 87.208 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 0.005476 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011467 0.00000