HEADER OXIDOREDUCTASE 17-JUL-03 1Q0Q TITLE CRYSTAL STRUCTURE OF DXR IN COMPLEX WITH THE SUBSTRATE 1-DEOXY-D- TITLE 2 XYLULOSE-5-PHOSPHATE 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, 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 5 16-AUG-23 1Q0Q 1 REMARK SEQADV REVDAT 4 03-OCT-18 1Q0Q 1 REMARK REVDAT 3 24-FEB-09 1Q0Q 1 VERSN REVDAT 2 01-MAR-05 1Q0Q 1 JRNL REVDAT 1 20-JUL-04 1Q0Q 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. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 6.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 5.1 REMARK 3 NUMBER OF REFLECTIONS : 61149 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3185 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 : 6060 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 122 REMARK 3 SOLVENT ATOMS : 639 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ; 0.007 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 1.136 ; 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 1Q0Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019770. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97818 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 61149 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.730 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 1Q0H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 200MM LI2SO4, 100MM BIS REMARK 280 -TRIS PH 6.5, MICROBATCH UNDER OIL, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 64.27650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.27650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 53.52850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.42300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 53.52850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.42300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.27650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 53.52850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.42300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.27650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 53.52850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.42300 REMARK 290 SMTRY3 8 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 300 REMARK: BIOLOGICAL HOMODIMER CONTAINED IN THE ASYMMETRIC UNIT 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: 6720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 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 465 HIS 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 SER B -1 REMARK 465 GLY B 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 480 ARG B 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 B 2099 O HOH B 2190 1.55 REMARK 500 OE1 GLN A 3 NH2 ARG A 29 1.77 REMARK 500 O HOH A 2144 O HOH A 2293 1.92 REMARK 500 O HOH B 2021 O HOH B 2262 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2132 O HOH B 2033 4556 1.79 REMARK 500 O HOH A 2103 O HOH B 2028 4556 1.94 REMARK 500 O HOH A 2052 O HOH A 2058 3655 2.13 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 ASP B 150 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 ASN A 167 56.80 -142.85 REMARK 500 SER A 258 168.64 157.38 REMARK 500 ASN B 24 57.83 -140.45 REMARK 500 SER B 50 57.57 39.43 REMARK 500 SER B 258 168.73 161.87 REMARK 500 ASP B 368 62.17 -155.54 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 DXP A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DXP B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 2002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q0H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SELENOMETHIONINE-LABELLED DXR IN COMPLEX WITH REMARK 900 FOSMIDOMYCIN REMARK 900 RELATED ID: 1Q0L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DXR IN COMPLEX WITH FOSMIDOMYCIN DBREF 1Q0Q A 1 398 UNP P45568 DXR_ECOLI 1 398 DBREF 1Q0Q B 1 398 UNP P45568 DXR_ECOLI 1 398 SEQADV 1Q0Q HIS A -7 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS A -6 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS A -5 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS A -4 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS A -3 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS A -2 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q SER A -1 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q GLY A 0 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS B -7 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS B -6 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS B -5 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS B -4 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS B -3 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q HIS B -2 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q SER B -1 UNP P45568 EXPRESSION TAG SEQADV 1Q0Q GLY B 0 UNP P45568 EXPRESSION TAG SEQRES 1 A 406 HIS HIS HIS HIS HIS HIS SER GLY MET 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 MET VAL GLU SEQRES 5 A 406 GLN CYS LEU GLU PHE SER PRO ARG TYR ALA VAL MET ASP SEQRES 6 A 406 ASP GLU ALA SER ALA LYS LEU LEU LYS THR MET 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 MET ALA ALA LEU GLU ASP VAL ASP GLN SEQRES 9 A 406 VAL MET 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 MET 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 MET THR PRO ASP GLN ALA CYS ARG HIS PRO ASN TRP SER SEQRES 18 A 406 MET GLY ARG LYS ILE SER VAL ASP SER ALA THR MET MET 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 MET GLU VAL LEU ILE HIS PRO SEQRES 21 A 406 GLN SER VAL ILE HIS SER MET VAL ARG TYR GLN ASP GLY SEQRES 22 A 406 SER VAL LEU ALA GLN LEU GLY GLU PRO ASP MET ARG THR SEQRES 23 A 406 PRO ILE ALA HIS THR MET 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 MET 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 MET ASP MET 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 MET ARG SEQRES 32 A 406 LEU ALA SER SEQRES 1 B 406 HIS HIS HIS HIS HIS HIS SER GLY MET LYS GLN LEU THR SEQRES 2 B 406 ILE LEU GLY SER THR GLY SER ILE GLY CYS SER THR LEU SEQRES 3 B 406 ASP VAL VAL ARG HIS ASN PRO GLU HIS PHE ARG VAL VAL SEQRES 4 B 406 ALA LEU VAL ALA GLY LYS ASN VAL THR ARG MET VAL GLU SEQRES 5 B 406 GLN CYS LEU GLU PHE SER PRO ARG TYR ALA VAL MET ASP SEQRES 6 B 406 ASP GLU ALA SER ALA LYS LEU LEU LYS THR MET LEU GLN SEQRES 7 B 406 GLN GLN GLY SER ARG THR GLU VAL LEU SER GLY GLN GLN SEQRES 8 B 406 ALA ALA CYS ASP MET ALA ALA LEU GLU ASP VAL ASP GLN SEQRES 9 B 406 VAL MET ALA ALA ILE VAL GLY ALA ALA GLY LEU LEU PRO SEQRES 10 B 406 THR LEU ALA ALA ILE ARG ALA GLY LYS THR ILE LEU LEU SEQRES 11 B 406 ALA ASN LYS GLU SER LEU VAL THR CYS GLY ARG LEU PHE SEQRES 12 B 406 MET ASP ALA VAL LYS GLN SER LYS ALA GLN LEU LEU PRO SEQRES 13 B 406 VAL ASP SER GLU HIS ASN ALA ILE PHE GLN SER LEU PRO SEQRES 14 B 406 GLN PRO ILE GLN HIS ASN LEU GLY TYR ALA ASP LEU GLU SEQRES 15 B 406 GLN ASN GLY VAL VAL SER ILE LEU LEU THR GLY SER GLY SEQRES 16 B 406 GLY PRO PHE ARG GLU THR PRO LEU ARG ASP LEU ALA THR SEQRES 17 B 406 MET THR PRO ASP GLN ALA CYS ARG HIS PRO ASN TRP SER SEQRES 18 B 406 MET GLY ARG LYS ILE SER VAL ASP SER ALA THR MET MET SEQRES 19 B 406 ASN LYS GLY LEU GLU TYR ILE GLU ALA ARG TRP LEU PHE SEQRES 20 B 406 ASN ALA SER ALA SER GLN MET GLU VAL LEU ILE HIS PRO SEQRES 21 B 406 GLN SER VAL ILE HIS SER MET VAL ARG TYR GLN ASP GLY SEQRES 22 B 406 SER VAL LEU ALA GLN LEU GLY GLU PRO ASP MET ARG THR SEQRES 23 B 406 PRO ILE ALA HIS THR MET ALA TRP PRO ASN ARG VAL ASN SEQRES 24 B 406 SER GLY VAL LYS PRO LEU ASP PHE CYS LYS LEU SER ALA SEQRES 25 B 406 LEU THR PHE ALA ALA PRO ASP TYR ASP ARG TYR PRO CYS SEQRES 26 B 406 LEU LYS LEU ALA MET GLU ALA PHE GLU GLN GLY GLN ALA SEQRES 27 B 406 ALA THR THR ALA LEU ASN ALA ALA ASN GLU ILE THR VAL SEQRES 28 B 406 ALA ALA PHE LEU ALA GLN GLN ILE ARG PHE THR ASP ILE SEQRES 29 B 406 ALA ALA LEU ASN LEU SER VAL LEU GLU LYS MET ASP MET SEQRES 30 B 406 ARG GLU PRO GLN CYS VAL ASP ASP VAL LEU SER VAL ASP SEQRES 31 B 406 ALA ASN ALA ARG GLU VAL ALA ARG LYS GLU VAL MET ARG SEQRES 32 B 406 LEU ALA SER HET DXP A 701 14 HET NDP A2001 48 HET DXP B 702 14 HET NDP B2002 48 HETNAM DXP 1-DEOXY-D-XYLULOSE-5-PHOSPHATE HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE FORMUL 3 DXP 2(C5 H11 O7 P) FORMUL 4 NDP 2(C21 H30 N7 O17 P3) FORMUL 7 HOH *639(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 GLN A 72 1 15 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 GLY A 132 1 9 HELIX 8 8 GLY A 132 LYS A 143 1 12 HELIX 9 9 ASP A 150 SER A 159 1 10 HELIX 10 10 PRO A 161 HIS A 166 1 6 HELIX 11 11 LEU A 173 ASN A 176 5 4 HELIX 12 12 PRO A 194 MET A 201 5 8 HELIX 13 13 THR A 202 ARG A 208 1 7 HELIX 14 14 GLY A 215 THR A 224 1 10 HELIX 15 15 MET A 225 ASN A 240 1 16 HELIX 16 16 SER A 242 SER A 244 5 3 HELIX 17 17 MET A 276 TRP A 286 1 11 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 MET A 367 1 14 HELIX 21 21 CYS A 374 LEU A 396 1 23 HELIX 22 22 GLY B 11 HIS B 23 1 13 HELIX 23 23 ASN B 38 SER B 50 1 13 HELIX 24 24 ASP B 58 GLN B 72 1 15 HELIX 25 25 GLY B 81 ALA B 90 1 10 HELIX 26 26 GLY B 103 ALA B 105 5 3 HELIX 27 27 GLY B 106 ALA B 116 1 11 HELIX 28 28 ASN B 124 GLY B 132 1 9 HELIX 29 29 GLY B 132 SER B 142 1 11 HELIX 30 30 ASP B 150 SER B 159 1 10 HELIX 31 31 PRO B 161 HIS B 166 1 6 HELIX 32 32 LEU B 173 ASN B 176 5 4 HELIX 33 33 PRO B 194 MET B 201 5 8 HELIX 34 34 THR B 202 ARG B 208 1 7 HELIX 35 35 GLY B 215 THR B 224 1 10 HELIX 36 36 MET B 225 ASN B 240 1 16 HELIX 37 37 SER B 242 SER B 244 5 3 HELIX 38 38 MET B 276 TRP B 286 1 11 HELIX 39 39 ASP B 298 LEU B 302 5 5 HELIX 40 40 TYR B 315 GLY B 328 1 14 HELIX 41 41 GLY B 328 ALA B 348 1 21 HELIX 42 42 THR B 354 MET B 367 1 14 HELIX 43 43 CYS B 374 LEU B 396 1 23 SHEET 1 A 7 GLU A 77 SER A 80 0 SHEET 2 A 7 TYR A 53 MET A 56 1 N ALA A 54 O LEU A 79 SHEET 3 A 7 PHE A 28 ALA A 35 1 N LEU A 33 O VAL A 55 SHEET 4 A 7 LYS A 2 LEU A 7 1 N LEU A 4 O VAL A 31 SHEET 5 A 7 GLN A 96 ALA A 99 1 O MET A 98 N LEU A 7 SHEET 6 A 7 THR A 119 LEU A 122 1 O THR A 119 N VAL A 97 SHEET 7 A 7 GLN A 145 PRO A 148 1 O LEU A 147 N ILE A 120 SHEET 1 B 8 MET A 246 ILE A 250 0 SHEET 2 B 8 VAL A 178 GLY A 185 1 N LEU A 183 O GLU A 247 SHEET 3 B 8 ILE A 256 TYR A 262 -1 O ARG A 261 N SER A 180 SHEET 4 B 8 VAL A 267 LEU A 271 -1 O LEU A 268 N VAL A 260 SHEET 5 B 8 VAL B 267 LEU B 271 -1 O VAL B 267 N LEU A 271 SHEET 6 B 8 ILE B 256 TYR B 262 -1 N VAL B 260 O LEU B 268 SHEET 7 B 8 VAL B 178 GLY B 185 -1 N SER B 180 O ARG B 261 SHEET 8 B 8 MET B 246 ILE B 250 1 O GLU B 247 N LEU B 183 SHEET 1 C 7 GLU B 77 SER B 80 0 SHEET 2 C 7 TYR B 53 MET B 56 1 N ALA B 54 O LEU B 79 SHEET 3 C 7 PHE B 28 ALA B 35 1 N LEU B 33 O VAL B 55 SHEET 4 C 7 LYS B 2 LEU B 7 1 N LEU B 4 O VAL B 31 SHEET 5 C 7 GLN B 96 ALA B 99 1 O MET B 98 N LEU B 7 SHEET 6 C 7 THR B 119 LEU B 122 1 O LEU B 121 N VAL B 97 SHEET 7 C 7 GLN B 145 PRO B 148 1 O LEU B 147 N ILE B 120 CISPEP 1 THR A 184 GLY A 185 0 6.36 CISPEP 2 TRP A 286 PRO A 287 0 6.57 CISPEP 3 THR B 184 GLY B 185 0 8.34 CISPEP 4 TRP B 286 PRO B 287 0 7.66 SITE 1 AC1 17 LYS A 125 ASP A 150 SER A 151 GLU A 152 SITE 2 AC1 17 SER A 186 HIS A 209 TRP A 212 ILE A 218 SITE 3 AC1 17 SER A 222 ASN A 227 LYS A 228 GLU A 231 SITE 4 AC1 17 MET A 276 NDP A2001 HOH A2093 HOH A2094 SITE 5 AC1 17 HOH A2110 SITE 1 AC2 16 LYS B 125 ASP B 150 SER B 151 GLU B 152 SITE 2 AC2 16 SER B 186 HIS B 209 TRP B 212 ILE B 218 SITE 3 AC2 16 SER B 222 ASN B 227 LYS B 228 GLU B 231 SITE 4 AC2 16 NDP B2002 HOH B2131 HOH B2132 HOH B2251 SITE 1 AC3 35 GLY A 8 THR A 10 GLY A 11 SER A 12 SITE 2 AC3 35 ILE A 13 ALA A 35 GLY A 36 LYS A 37 SITE 3 AC3 35 ASN A 38 ASP A 57 ALA A 100 ILE A 101 SITE 4 AC3 35 VAL A 102 ALA A 123 ASN A 124 LYS A 125 SITE 5 AC3 35 GLU A 126 ASP A 150 MET A 214 GLY A 215 SITE 6 AC3 35 ILE A 218 MET A 276 DXP A 701 HOH A2003 SITE 7 AC3 35 HOH A2004 HOH A2009 HOH A2018 HOH A2019 SITE 8 AC3 35 HOH A2022 HOH A2035 HOH A2067 HOH A2114 SITE 9 AC3 35 HOH A2187 HOH A2190 HOH A2191 SITE 1 AC4 36 GLY B 8 THR B 10 GLY B 11 SER B 12 SITE 2 AC4 36 ILE B 13 ALA B 35 GLY B 36 LYS B 37 SITE 3 AC4 36 ASN B 38 ASP B 57 ALA B 100 ILE B 101 SITE 4 AC4 36 VAL B 102 ALA B 105 ALA B 123 ASN B 124 SITE 5 AC4 36 LYS B 125 GLU B 126 ASP B 150 MET B 214 SITE 6 AC4 36 GLY B 215 ILE B 218 MET B 276 DXP B 702 SITE 7 AC4 36 HOH B2043 HOH B2044 HOH B2045 HOH B2046 SITE 8 AC4 36 HOH B2050 HOH B2063 HOH B2065 HOH B2075 SITE 9 AC4 36 HOH B2096 HOH B2159 HOH B2270 HOH B2273 CRYST1 107.057 122.846 128.553 90.00 90.00 90.00 C 2 2 21 16 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 0.009341 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007779 0.00000