PDB Short entry for 2JCV HEADER OXIDOREDUCTASE 04-JAN-07 2JCV TITLE X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, TITLE 2 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH TITLE 3 FOSMIDOMYCIN AND NADPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 2-389; COMPND 5 SYNONYM: DXP REDUCTOISOMERASE, 1-DEOXYXYLULOSE-5-PHOSPHATE COMPND 6 REDUCTOISOMERASE, 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE SYNTHASE; COMPND 7 EC: 1.1.1.267; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET101D-TOPO KEYWDS OXIDOREDUCTASE, DOXP/MEP PATHWAY, ISOPRENE BIOSYNTHESIS, 1-DEOXY-D- KEYWDS 2 XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, NADP, RV2870C, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.M.HENRIKSSON,T.UNGE,T.A.JONES,S.L.MOWBRAY REVDAT 5 13-DEC-23 2JCV 1 REMARK REVDAT 4 24-FEB-09 2JCV 1 VERSN REVDAT 3 10-JUL-07 2JCV 1 JRNL REVDAT 2 22-MAY-07 2JCV 1 JRNL HETATM REVDAT 1 08-MAY-07 2JCV 0 JRNL AUTH L.M.HENRIKSSON,T.UNGE,J.CARLSSON,J.AQVIST,S.L.MOWBRAY, JRNL AUTH 2 T.A.JONES JRNL TITL STRUCTURES OF MYCOBACTERIUM TUBERCULOSIS 1-DEOXY-D- JRNL TITL 2 XYLULOSE-5-PHOSPHATE REDUCTOISOMERASE PROVIDE NEW INSIGHTS JRNL TITL 3 INTO CATALYSIS. JRNL REF J.BIOL.CHEM. V. 282 19905 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17491006 JRNL DOI 10.1074/JBC.M701935200 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 35057 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1848 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2149 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1720 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5562 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 117 REMARK 3 SOLVENT ATOMS : 521 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.96000 REMARK 3 B33 (A**2) : -1.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.18000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.282 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.198 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 : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5820 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7974 ; 1.233 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 762 ; 5.273 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 231 ;35.381 ;23.593 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 845 ;13.203 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;18.254 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 933 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4417 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2764 ; 0.191 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4027 ; 0.292 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 492 ; 0.168 ; 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): 71 ; 0.205 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.156 ; 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): 3776 ; 0.504 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6029 ; 0.962 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2044 ; 1.632 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1945 ; 2.678 ; 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 : 1.40 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 2JCV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1290030884. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.940 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36913 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27000 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2C82 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 32.73800 REMARK 290 SMTRY3 2 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: PQS 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 THR A -8 REMARK 465 MET A -7 REMARK 465 ALA 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 HIS A 0 REMARK 465 VAL A 1 REMARK 465 THR A 2 REMARK 465 ASN A 3 REMARK 465 SER A 4 REMARK 465 THR A 5 REMARK 465 ASP A 6 REMARK 465 GLY A 7 REMARK 465 ARG A 8 REMARK 465 ALA A 9 REMARK 465 ASP A 10 REMARK 465 THR B -8 REMARK 465 MET B -7 REMARK 465 ALA 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 HIS B 0 REMARK 465 VAL B 1 REMARK 465 THR B 2 REMARK 465 ASN B 3 REMARK 465 SER B 4 REMARK 465 THR B 5 REMARK 465 ASP B 6 REMARK 465 GLY B 7 REMARK 465 ARG B 8 REMARK 465 ALA B 9 REMARK 465 ASP B 10 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 NH2 ARG B 38 O HOH B 2020 1.81 REMARK 500 O HOH A 2030 O HOH A 2094 1.98 REMARK 500 O HOH A 2030 O HOH A 2084 2.00 REMARK 500 O HOH A 2113 O HOH A 2167 2.10 REMARK 500 OE1 GLU B 310 O HOH B 2217 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 249 165.54 161.62 REMARK 500 ALA B 197 13.05 -69.56 REMARK 500 SER B 249 168.19 165.43 REMARK 500 ASP B 266 104.91 -179.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2035 DISTANCE = 5.85 ANGSTROMS REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOM A1390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A1391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B1390 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2C82 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5 -PHOSPHATE REDUCTOISOMERASE, REMARK 900 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS REMARK 900 RELATED ID: 2JCX RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF MUTANT 1-DEOXY-D- XYLULOSE 5-PHOSPHATE REMARK 900 REDUCTOISOMERASE, DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN REMARK 900 COMPLEX WITH FOSMIDOMYCIN AND NADPH REMARK 900 RELATED ID: 2JCY RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF MUTANT 1-DEOXY-D- XYLULOSE 5-PHOSPHATE REMARK 900 REDUCTOISOMERASE, DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS REMARK 900 RELATED ID: 2JCZ RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5 -PHOSPHATE REDUCTOISOMERASE, REMARK 900 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH REMARK 900 FOSMIDOMYCIN, MANGANESE AND NADPH REMARK 900 RELATED ID: 2JD0 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF MUTANT 1-DEOXY-D- XYLULOSE 5-PHOSPHATE REMARK 900 REDUCTOISOMERASE, DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN REMARK 900 COMPLEX WITH NADPH REMARK 900 RELATED ID: 2JD1 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5 -PHOSPHATE REDUCTOISOMERASE, REMARK 900 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH REMARK 900 MANGANESE AND NADPH REMARK 900 RELATED ID: 2JD2 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5 -PHOSPHATE REDUCTOISOMERASE, REMARK 900 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH REMARK 900 MANGANESE DBREF 2JCV A -8 1 PDB 2JCV 2JCV -8 1 DBREF 2JCV A 2 389 UNP P64012 DXR_MYCTU 2 389 DBREF 2JCV B -8 1 PDB 2JCV 2JCV -8 1 DBREF 2JCV B 2 389 UNP P64012 DXR_MYCTU 2 389 SEQRES 1 A 398 THR MET ALA HIS HIS HIS HIS HIS HIS VAL THR ASN SER SEQRES 2 A 398 THR ASP GLY ARG ALA ASP GLY ARG LEU ARG VAL VAL VAL SEQRES 3 A 398 LEU GLY SER THR GLY SER ILE GLY THR GLN ALA LEU GLN SEQRES 4 A 398 VAL ILE ALA ASP ASN PRO ASP ARG PHE GLU VAL VAL GLY SEQRES 5 A 398 LEU ALA ALA GLY GLY ALA HIS LEU ASP THR LEU LEU ARG SEQRES 6 A 398 GLN ARG ALA GLN THR GLY VAL THR ASN ILE ALA VAL ALA SEQRES 7 A 398 ASP GLU HIS ALA ALA GLN ARG VAL GLY ASP ILE PRO TYR SEQRES 8 A 398 HIS GLY SER ASP ALA ALA THR ARG LEU VAL GLU GLN THR SEQRES 9 A 398 GLU ALA ASP VAL VAL LEU ASN ALA LEU VAL GLY ALA LEU SEQRES 10 A 398 GLY LEU ARG PRO THR LEU ALA ALA LEU LYS THR GLY ALA SEQRES 11 A 398 ARG LEU ALA LEU ALA ASN LYS GLU SER LEU VAL ALA GLY SEQRES 12 A 398 GLY SER LEU VAL LEU ARG ALA ALA ARG PRO GLY GLN ILE SEQRES 13 A 398 VAL PRO VAL ASP SER GLU HIS SER ALA LEU ALA GLN CYS SEQRES 14 A 398 LEU ARG GLY GLY THR PRO ASP GLU VAL ALA LYS LEU VAL SEQRES 15 A 398 LEU THR ALA SER GLY GLY PRO PHE ARG GLY TRP SER ALA SEQRES 16 A 398 ALA ASP LEU GLU HIS VAL THR PRO GLU GLN ALA GLY ALA SEQRES 17 A 398 HIS PRO THR TRP SER MET GLY PRO MET ASN THR LEU ASN SEQRES 18 A 398 SER ALA SER LEU VAL ASN LYS GLY LEU GLU VAL ILE GLU SEQRES 19 A 398 THR HIS LEU LEU PHE GLY ILE PRO TYR ASP ARG ILE ASP SEQRES 20 A 398 VAL VAL VAL HIS PRO GLN SER ILE ILE HIS SER MET VAL SEQRES 21 A 398 THR PHE ILE ASP GLY SER THR ILE ALA GLN ALA SER PRO SEQRES 22 A 398 PRO ASP MET LYS LEU PRO ILE SER LEU ALA LEU GLY TRP SEQRES 23 A 398 PRO ARG ARG VAL SER GLY ALA ALA ALA ALA CYS ASP PHE SEQRES 24 A 398 HIS THR ALA SER SER TRP GLU PHE GLU PRO LEU ASP THR SEQRES 25 A 398 ASP VAL PHE PRO ALA VAL GLU LEU ALA ARG GLN ALA GLY SEQRES 26 A 398 VAL ALA GLY GLY CYS MET THR ALA VAL TYR ASN ALA ALA SEQRES 27 A 398 ASN GLU GLU ALA ALA ALA ALA PHE LEU ALA GLY ARG ILE SEQRES 28 A 398 GLY PHE PRO ALA ILE VAL GLY ILE ILE ALA ASP VAL LEU SEQRES 29 A 398 HIS ALA ALA ASP GLN TRP ALA VAL GLU PRO ALA THR VAL SEQRES 30 A 398 ASP ASP VAL LEU ASP ALA GLN ARG TRP ALA ARG GLU ARG SEQRES 31 A 398 ALA GLN ARG ALA VAL SER GLY MET SEQRES 1 B 398 THR MET ALA HIS HIS HIS HIS HIS HIS VAL THR ASN SER SEQRES 2 B 398 THR ASP GLY ARG ALA ASP GLY ARG LEU ARG VAL VAL VAL SEQRES 3 B 398 LEU GLY SER THR GLY SER ILE GLY THR GLN ALA LEU GLN SEQRES 4 B 398 VAL ILE ALA ASP ASN PRO ASP ARG PHE GLU VAL VAL GLY SEQRES 5 B 398 LEU ALA ALA GLY GLY ALA HIS LEU ASP THR LEU LEU ARG SEQRES 6 B 398 GLN ARG ALA GLN THR GLY VAL THR ASN ILE ALA VAL ALA SEQRES 7 B 398 ASP GLU HIS ALA ALA GLN ARG VAL GLY ASP ILE PRO TYR SEQRES 8 B 398 HIS GLY SER ASP ALA ALA THR ARG LEU VAL GLU GLN THR SEQRES 9 B 398 GLU ALA ASP VAL VAL LEU ASN ALA LEU VAL GLY ALA LEU SEQRES 10 B 398 GLY LEU ARG PRO THR LEU ALA ALA LEU LYS THR GLY ALA SEQRES 11 B 398 ARG LEU ALA LEU ALA ASN LYS GLU SER LEU VAL ALA GLY SEQRES 12 B 398 GLY SER LEU VAL LEU ARG ALA ALA ARG PRO GLY GLN ILE SEQRES 13 B 398 VAL PRO VAL ASP SER GLU HIS SER ALA LEU ALA GLN CYS SEQRES 14 B 398 LEU ARG GLY GLY THR PRO ASP GLU VAL ALA LYS LEU VAL SEQRES 15 B 398 LEU THR ALA SER GLY GLY PRO PHE ARG GLY TRP SER ALA SEQRES 16 B 398 ALA ASP LEU GLU HIS VAL THR PRO GLU GLN ALA GLY ALA SEQRES 17 B 398 HIS PRO THR TRP SER MET GLY PRO MET ASN THR LEU ASN SEQRES 18 B 398 SER ALA SER LEU VAL ASN LYS GLY LEU GLU VAL ILE GLU SEQRES 19 B 398 THR HIS LEU LEU PHE GLY ILE PRO TYR ASP ARG ILE ASP SEQRES 20 B 398 VAL VAL VAL HIS PRO GLN SER ILE ILE HIS SER MET VAL SEQRES 21 B 398 THR PHE ILE ASP GLY SER THR ILE ALA GLN ALA SER PRO SEQRES 22 B 398 PRO ASP MET LYS LEU PRO ILE SER LEU ALA LEU GLY TRP SEQRES 23 B 398 PRO ARG ARG VAL SER GLY ALA ALA ALA ALA CYS ASP PHE SEQRES 24 B 398 HIS THR ALA SER SER TRP GLU PHE GLU PRO LEU ASP THR SEQRES 25 B 398 ASP VAL PHE PRO ALA VAL GLU LEU ALA ARG GLN ALA GLY SEQRES 26 B 398 VAL ALA GLY GLY CYS MET THR ALA VAL TYR ASN ALA ALA SEQRES 27 B 398 ASN GLU GLU ALA ALA ALA ALA PHE LEU ALA GLY ARG ILE SEQRES 28 B 398 GLY PHE PRO ALA ILE VAL GLY ILE ILE ALA ASP VAL LEU SEQRES 29 B 398 HIS ALA ALA ASP GLN TRP ALA VAL GLU PRO ALA THR VAL SEQRES 30 B 398 ASP ASP VAL LEU ASP ALA GLN ARG TRP ALA ARG GLU ARG SEQRES 31 B 398 ALA GLN ARG ALA VAL SER GLY MET HET FOM A1390 11 HET NDP A1391 48 HET SO4 A1392 5 HET NDP B1390 48 HET SO4 B1391 5 HETNAM FOM 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM SO4 SULFATE ION HETSYN FOM FOSMIDOMYCIN FORMUL 3 FOM C4 H10 N O5 P FORMUL 4 NDP 2(C21 H30 N7 O17 P3) FORMUL 5 SO4 2(O4 S 2-) FORMUL 8 HOH *521(H2 O) HELIX 1 1 GLY A 22 ASP A 34 1 13 HELIX 2 2 LEU A 51 THR A 61 1 11 HELIX 3 3 ASP A 70 VAL A 77 1 8 HELIX 4 4 ASP A 86 GLN A 94 1 9 HELIX 5 5 LEU A 108 LYS A 118 1 11 HELIX 6 6 LYS A 128 ALA A 133 1 6 HELIX 7 7 GLY A 135 ALA A 141 1 7 HELIX 8 8 ASP A 151 GLY A 163 1 13 HELIX 9 9 SER A 185 GLU A 190 1 6 HELIX 10 10 THR A 193 ALA A 197 1 5 HELIX 11 11 GLY A 206 ALA A 214 1 9 HELIX 12 12 LEU A 216 PHE A 230 1 15 HELIX 13 13 MET A 267 LEU A 275 1 9 HELIX 14 14 PRO A 307 ALA A 318 1 12 HELIX 15 15 CYS A 321 LEU A 338 1 18 HELIX 16 16 GLY A 343 ALA A 357 1 15 HELIX 17 17 VAL A 368 SER A 387 1 20 HELIX 18 18 GLY B 22 ASP B 34 1 13 HELIX 19 19 LEU B 51 THR B 61 1 11 HELIX 20 20 ASP B 70 VAL B 77 1 8 HELIX 21 21 ASP B 86 GLN B 94 1 9 HELIX 22 22 LEU B 108 LYS B 118 1 11 HELIX 23 23 LYS B 128 ALA B 133 1 6 HELIX 24 24 GLY B 135 ALA B 141 1 7 HELIX 25 25 ASP B 151 GLY B 163 1 13 HELIX 26 26 SER B 185 GLU B 190 1 6 HELIX 27 27 THR B 193 ALA B 197 1 5 HELIX 28 28 GLY B 206 ALA B 214 1 9 HELIX 29 29 LEU B 216 PHE B 230 1 15 HELIX 30 30 MET B 267 LEU B 275 1 9 HELIX 31 31 PRO B 307 ALA B 318 1 12 HELIX 32 32 CYS B 321 LEU B 338 1 18 HELIX 33 33 GLY B 343 ALA B 357 1 15 HELIX 34 34 VAL B 368 SER B 387 1 20 SHEET 1 AA 7 TYR A 82 HIS A 83 0 SHEET 2 AA 7 ASN A 65 VAL A 68 1 O ILE A 66 N TYR A 82 SHEET 3 AA 7 ARG A 38 ALA A 46 1 O LEU A 44 N ALA A 67 SHEET 4 AA 7 LEU A 13 LEU A 18 1 O LEU A 13 N GLU A 40 SHEET 5 AA 7 ASP A 98 ASN A 102 1 O VAL A 99 N VAL A 16 SHEET 6 AA 7 ALA A 121 LEU A 125 1 O ARG A 122 N VAL A 100 SHEET 7 AA 7 GLN A 146 PRO A 149 1 O VAL A 148 N LEU A 125 SHEET 1 AB 8 ARG A 236 VAL A 241 0 SHEET 2 AB 8 ALA A 170 ALA A 176 1 O LEU A 172 N ASP A 238 SHEET 3 AB 8 MET A 250 PHE A 253 -1 O MET A 250 N VAL A 173 SHEET 4 AB 8 SER A 257 ALA A 262 -1 O ILE A 259 N VAL A 251 SHEET 5 AB 8 SER B 257 ALA B 262 -1 O THR B 258 N ALA A 262 SHEET 6 AB 8 MET B 250 PHE B 253 -1 N MET B 250 O ILE B 259 SHEET 7 AB 8 ALA B 170 ALA B 176 -1 N ALA B 170 O THR B 252 SHEET 8 AB 8 ARG B 236 VAL B 241 1 O ASP B 238 N LEU B 174 SHEET 1 AC 2 ALA A 293 PHE A 298 0 SHEET 2 AC 2 ALA B 293 PHE B 298 -1 O SER B 294 N PHE A 298 SHEET 1 BA 7 TYR B 82 HIS B 83 0 SHEET 2 BA 7 ASN B 65 VAL B 68 1 O ILE B 66 N TYR B 82 SHEET 3 BA 7 ARG B 38 ALA B 46 1 O LEU B 44 N ALA B 67 SHEET 4 BA 7 LEU B 13 LEU B 18 1 O LEU B 13 N GLU B 40 SHEET 5 BA 7 ASP B 98 ASN B 102 1 O VAL B 99 N VAL B 16 SHEET 6 BA 7 ALA B 121 LEU B 125 1 O ARG B 122 N VAL B 100 SHEET 7 BA 7 GLN B 146 PRO B 149 1 O VAL B 148 N LEU B 125 CISPEP 1 TRP A 277 PRO A 278 0 5.94 CISPEP 2 TRP B 277 PRO B 278 0 2.62 SITE 1 AC1 4 ARG A 162 TRP A 277 PRO A 278 HOH A2116 SITE 1 AC2 8 ALA B 176 SER B 177 SER B 213 ASN B 218 SITE 2 AC2 8 LYS B 219 HOH B2265 HOH B2266 HOH B2267 SITE 1 AC3 16 SER A 152 GLU A 153 ALA A 176 SER A 177 SITE 2 AC3 16 HIS A 200 TRP A 203 SER A 213 ASN A 218 SITE 3 AC3 16 LYS A 219 GLU A 222 MET A 267 NDP A1391 SITE 4 AC3 16 HOH A2238 HOH A2239 HOH A2240 HOH A2241 SITE 1 AC4 35 GLY A 19 THR A 21 GLY A 22 SER A 23 SITE 2 AC4 35 ILE A 24 ALA A 46 GLY A 47 GLY A 48 SITE 3 AC4 35 ALA A 49 HIS A 50 ALA A 69 ALA A 103 SITE 4 AC4 35 LEU A 104 ALA A 126 ASN A 127 LYS A 128 SITE 5 AC4 35 GLU A 129 MET A 205 GLY A 206 PRO A 207 SITE 6 AC4 35 ASN A 209 MET A 267 FOM A1390 HOH A2144 SITE 7 AC4 35 HOH A2242 HOH A2243 HOH A2244 HOH A2245 SITE 8 AC4 35 HOH A2246 HOH A2247 HOH A2248 HOH A2249 SITE 9 AC4 35 HOH A2250 HOH A2251 HOH A2253 SITE 1 AC5 22 GLY B 19 THR B 21 GLY B 22 SER B 23 SITE 2 AC5 22 ILE B 24 ALA B 46 GLY B 47 GLY B 48 SITE 3 AC5 22 ALA B 49 HIS B 50 ALA B 69 ALA B 103 SITE 4 AC5 22 LEU B 104 LEU B 108 ALA B 126 ASN B 127 SITE 5 AC5 22 LYS B 128 HOH B2071 HOH B2102 HOH B2261 SITE 6 AC5 22 HOH B2263 HOH B2264 CRYST1 67.348 65.476 86.086 90.00 101.56 90.00 P 1 21 1 4 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 0.014848 0.000000 0.003037 0.00000 SCALE2 0.000000 0.015273 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011857 0.00000 MTRIX1 1 -0.480300 0.864400 0.148900 0.44280 1 MTRIX2 1 0.854600 0.422900 0.301500 -23.77070 1 MTRIX3 1 0.197700 0.272000 -0.941800 118.31020 1