HEADER OXIDOREDUCTASE 04-JAN-07 2JD1 TITLE X-RAY STRUCTURE OF 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, TITLE 2 DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH TITLE 3 MANGANESE 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 2JD1 1 LINK REVDAT 4 24-FEB-09 2JD1 1 VERSN REVDAT 3 10-JUL-07 2JD1 1 JRNL REVDAT 2 22-MAY-07 2JD1 1 JRNL HETATM REVDAT 1 08-MAY-07 2JD1 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. 2.00 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) : 35.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 46754 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 : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2493 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) : 3407 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 181 REMARK 3 BIN FREE R VALUE : 0.2600 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 : 65 REMARK 3 SOLVENT ATOMS : 507 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : 0.73000 REMARK 3 B33 (A**2) : -0.95000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.188 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 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 : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5795 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7918 ; 1.166 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 766 ; 5.180 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 232 ;33.660 ;23.534 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 851 ;13.450 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;18.725 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 927 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4417 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2877 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3992 ; 0.294 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 501 ; 0.153 ; 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): 82 ; 0.198 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.135 ; 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): 3794 ; 0.507 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6052 ; 0.941 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2001 ; 1.548 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1866 ; 2.485 ; 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 2JD1 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_1290030889. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-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 : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 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 : 49295 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48000 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: 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 32.44400 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 CE MET B 267 O HOH B 2121 1.92 REMARK 500 O HOH B 2030 O HOH B 2031 2.05 REMARK 500 O HOH B 2100 O HOH B 2102 2.08 REMARK 500 O HOH B 2131 O HOH B 2133 2.10 REMARK 500 NH2 ARG A 384 O HOH A 2209 2.16 REMARK 500 OE2 GLU A 225 O HOH A 2125 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 ASN A 65 84.22 -67.90 REMARK 500 SER A 249 168.31 161.76 REMARK 500 ASP A 266 111.02 -166.22 REMARK 500 VAL B 77 -52.15 -120.29 REMARK 500 SER B 249 171.17 163.46 REMARK 500 ASP B 266 109.37 -176.47 REMARK 500 ASP B 266 110.28 -176.47 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 A2016 DISTANCE = 6.74 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1391 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 151 OD2 REMARK 620 2 GLU A 153 OE1 89.0 REMARK 620 3 GLU A 222 OE2 102.8 94.6 REMARK 620 4 HOH A2216 O 159.4 94.0 97.3 REMARK 620 5 HOH A2217 O 86.1 103.8 159.8 73.4 REMARK 620 6 HOH A2218 O 96.8 169.9 92.2 77.6 68.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1390 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 151 OD2 REMARK 620 2 GLU B 153 OE2 88.1 REMARK 620 3 GLU B 222 OE1 82.8 94.1 REMARK 620 4 HOH B2281 O 96.9 174.9 87.2 REMARK 620 5 HOH B2282 O 171.9 85.5 102.6 89.4 REMARK 620 6 HOH B2283 O 92.0 91.0 172.5 88.1 83.2 REMARK 620 N 1 2 3 4 5 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 MN A1391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1393 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B1390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A1390 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: 2JCV 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 AND NADPH 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: 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 2JD1 A -8 1 PDB 2JD1 2JD1 -8 1 DBREF 2JD1 A 2 389 UNP P64012 DXR_MYCTU 2 389 DBREF 2JD1 B -8 1 PDB 2JD1 2JD1 -8 1 DBREF 2JD1 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 NDP A1390 48 HET MN A1391 1 HET SO4 A1392 5 HET SO4 A1393 5 HET MN B1390 1 HET SO4 B1391 5 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION FORMUL 3 NDP C21 H30 N7 O17 P3 FORMUL 4 MN 2(MN 2+) FORMUL 5 SO4 3(O4 S 2-) FORMUL 9 HOH *507(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 LINK OD2 ASP A 151 MN MN A1391 1555 1555 2.18 LINK OE1 GLU A 153 MN MN A1391 1555 1555 2.19 LINK OE2 GLU A 222 MN MN A1391 1555 1555 2.19 LINK MN MN A1391 O HOH A2216 1555 1555 2.20 LINK MN MN A1391 O HOH A2217 1555 1555 2.20 LINK MN MN A1391 O HOH A2218 1555 1555 2.21 LINK OD2 ASP B 151 MN MN B1390 1555 1555 2.19 LINK OE2 GLU B 153 MN MN B1390 1555 1555 2.21 LINK OE1 GLU B 222 MN MN B1390 1555 1555 2.18 LINK MN MN B1390 O HOH B2281 1555 1555 2.21 LINK MN MN B1390 O HOH B2282 1555 1555 2.21 LINK MN MN B1390 O HOH B2283 1555 1555 2.21 CISPEP 1 TRP A 277 PRO A 278 0 1.68 CISPEP 2 TRP B 277 PRO B 278 0 6.80 SITE 1 AC1 7 LYS A 128 ASP A 151 GLU A 153 GLU A 222 SITE 2 AC1 7 HOH A2216 HOH A2217 HOH A2218 SITE 1 AC2 10 ALA A 176 SER A 177 HIS A 200 SER A 213 SITE 2 AC2 10 ASN A 218 LYS A 219 HOH A2106 HOH A2216 SITE 3 AC2 10 HOH A2219 HOH A2220 SITE 1 AC3 5 ARG A 162 TRP A 277 PRO A 278 HOH A2092 SITE 2 AC3 5 HOH A2221 SITE 1 AC4 6 ASP B 151 GLU B 153 GLU B 222 HOH B2281 SITE 2 AC4 6 HOH B2282 HOH B2283 SITE 1 AC5 9 ALA B 176 SER B 177 SER B 213 ASN B 218 SITE 2 AC5 9 LYS B 219 HOH B2282 HOH B2284 HOH B2285 SITE 3 AC5 9 HOH B2286 SITE 1 AC6 27 GLY A 19 THR A 21 GLY A 22 SER A 23 SITE 2 AC6 27 ILE A 24 ALA A 46 GLY A 47 GLY A 48 SITE 3 AC6 27 ALA A 49 HIS A 50 ALA A 69 ALA A 103 SITE 4 AC6 27 LEU A 104 ALA A 126 ASN A 127 LYS A 128 SITE 5 AC6 27 GLU A 129 ASP A 151 MET A 205 GLY A 206 SITE 6 AC6 27 ASN A 209 MET A 267 HOH A2001 HOH A2119 SITE 7 AC6 27 HOH A2212 HOH A2213 HOH A2214 CRYST1 67.332 64.888 86.059 90.00 101.72 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 0.014852 0.000000 0.003081 0.00000 SCALE2 0.000000 0.015411 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011867 0.00000 MTRIX1 1 -0.498000 0.854900 0.145300 22.68090 1 MTRIX2 1 0.844700 0.440400 0.304300 -20.17660 1 MTRIX3 1 0.196100 0.274300 -0.941400 35.57580 1