HEADER OXIDOREDUCTASE 08-DEC-10 2Y1C 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. 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 HAMAP, 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-STAR (DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET101D-TOPO KEYWDS OXIDOREDUCTASE, DOXP/MEP PATHWAY EXPDTA X-RAY DIFFRACTION AUTHOR L.M.HENRIKSSON,A.M.S.LARSSON,T.BERGFORS,C.BJORKELID,T.UNGE, AUTHOR 2 S.L.MOWBRAY,T.A.JONES REVDAT 3 20-DEC-23 2Y1C 1 REMARK LINK REVDAT 2 03-AUG-11 2Y1C 1 JRNL REMARK VERSN REVDAT 1 29-JUN-11 2Y1C 0 JRNL AUTH M.ANDALOUSSI,L.M.HENRIKSSON,A.WIECKOWSKA,M.LINDH, JRNL AUTH 2 C.BJORKELID,A.M.S.LARSSON,H.IYER,B.R.SRINIVASA,T.BERGFORS, JRNL AUTH 3 T.UNGE,S.L.MOWBRAY,M.LARHED,T.A.JONES,A.KARLEN JRNL TITL DESIGN, SYNTHESIS AND X-RAY CRYSTALLOGRAPHIC STUDIES OF JRNL TITL 2 ALPHA-ARYL SUBSTITUTED FOSMIDOMYCIN ANALOGUES AS INHIBITORS JRNL TITL 3 OF MYCOBACTERIUM TUBERCULOSIS 1-DEOXY-D-XYLULOSE-5-PHOSPHATE JRNL TITL 4 REDUCTOISOMERASE JRNL REF J.MED.CHEM V. 54 4964 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21678907 JRNL DOI 10.1021/JM2000085 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.M.HENRIKSSON,C.BJORKELID,S.L.MOWBRAY,T.UNGE REMARK 1 TITL THE 1.9 A RESOLUTION STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS REMARK 1 TITL 2 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, A POTENTIAL REMARK 1 TITL 3 DRUG TARGET. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 62 807 2006 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 16790937 REMARK 1 DOI 10.1107/S0907444906019196 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.M.HENRIKSSON,T.UNGE,J.CARLSSON,J.AQVIST,S.L.MOWBRAY, REMARK 1 AUTH 2 T.A.JONES REMARK 1 TITL STRUCTURES OF MYCOBACTERIUM TUBERCULOSIS REMARK 1 TITL 2 1-DEOXY-D-XYLULOSE-5-PHOSPHATE REDUCTOISOMERASE PROVIDE NEW REMARK 1 TITL 3 INSIGHTS INTO CATALYSIS. REMARK 1 REF J.BIOL.CHEM. V. 282 19905 2007 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 17491006 REMARK 1 DOI 10.1074/JBC.M701935200 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 55426 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2943 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4010 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 220 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5505 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 473 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.78000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.90000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.166 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.618 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5643 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7695 ; 1.124 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 752 ; 5.327 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 226 ;34.230 ;23.584 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 835 ;13.669 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;18.622 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 908 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4308 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2863 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3888 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 476 ; 0.169 ; 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): 73 ; 0.183 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.110 ; 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): 3832 ; 0.639 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5960 ; 1.098 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2030 ; 1.590 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1735 ; 2.580 ; 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. A70-A76 HAVE BEEN REMOVED. REMARK 4 REMARK 4 2Y1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1290046604. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 110 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) : 0.955 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 : 58370 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 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) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45000 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 2JD2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 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 33.73850 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.6 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 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 ASP A 70 REMARK 465 GLU A 71 REMARK 465 HIS A 72 REMARK 465 ALA A 73 REMARK 465 ALA A 74 REMARK 465 GLN A 75 REMARK 465 ARG A 76 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 O HOH B 2135 O HOH B 2277 1.67 REMARK 500 O HOH A 2167 O HOH A 2168 1.86 REMARK 500 O HOH B 2074 O HOH B 2084 1.88 REMARK 500 O HOH B 2031 O HOH B 2086 1.98 REMARK 500 N ASP B 86 O HOH B 2081 1.99 REMARK 500 O HOH B 2105 O HOH B 2127 2.18 REMARK 500 NH2 ARG B 38 O HOH B 2026 2.18 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 HIS A 50 38.41 -94.82 REMARK 500 ASP A 79 41.70 -105.38 REMARK 500 ALA A 170 -62.01 -90.02 REMARK 500 SER A 249 169.08 165.13 REMARK 500 ASP A 266 109.56 -169.94 REMARK 500 PRO B 201 79.97 -44.19 REMARK 500 THR B 202 19.79 -152.05 REMARK 500 TRP B 203 -51.73 -146.66 REMARK 500 MET B 205 -65.06 -138.99 REMARK 500 SER B 249 174.46 174.72 REMARK 500 ASP B 266 111.10 -169.37 REMARK 500 PHE B 306 72.11 -115.45 REMARK 500 REMARK 500 REMARK: NULL 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 A1390 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 151 OD2 REMARK 620 2 GLU A 153 OE1 85.6 REMARK 620 3 GLU A 222 OE2 79.7 93.9 REMARK 620 4 HOH A2166 O 99.6 173.9 90.1 REMARK 620 5 HOH A2167 O 173.1 88.9 96.5 86.1 REMARK 620 6 HOH A2168 O 133.7 87.5 146.5 86.7 50.0 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 OE1 87.6 REMARK 620 3 GLU B 222 OE2 86.6 100.0 REMARK 620 4 HOH B2303 O 90.6 175.1 84.5 REMARK 620 5 HOH B2304 O 174.6 88.9 89.9 93.2 REMARK 620 6 HOH B2305 O 119.1 89.6 153.1 87.2 65.0 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 A 1390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 1390 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Y1G 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 A 3, REMARK 900 4-DICHLOROPHENYL-SUBSTITUTED FR900098 ANALOGUE AND MANGANESE. REMARK 900 RELATED ID: 2Y1D 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 A 3, REMARK 900 4-DICHLOROPHENYL-SUBSTITUTED FOSMIDOMYCIN ANALOGUE AND MANGANESE. REMARK 900 RELATED ID: 2Y1F 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 A 3, REMARK 900 4-DICHLOROPHENYL-SUBSTITUTED FOSMIDOMYCIN ANALOGUE, MANGANESE AND REMARK 900 NADPH. REMARK 900 RELATED ID: 2Y1E 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 2Y1C A 1 389 UNP A2VLK3 A2VLK3_MYCTU 24 412 DBREF 2Y1C B 1 389 UNP A2VLK3 A2VLK3_MYCTU 24 412 SEQADV 2Y1C THR A -8 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C MET A -7 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C ALA A -6 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS A -5 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS A -4 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS A -3 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS A -2 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS A -1 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS A 0 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C THR B -8 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C MET B -7 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C ALA B -6 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS B -5 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS B -4 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS B -3 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS B -2 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS B -1 UNP A2VLK3 EXPRESSION TAG SEQADV 2Y1C HIS B 0 UNP A2VLK3 EXPRESSION TAG 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 MN A1390 1 HET MN B1390 1 HETNAM MN MANGANESE (II) ION FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *473(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 86 GLN A 94 1 9 HELIX 4 4 LEU A 108 LYS A 118 1 11 HELIX 5 5 LYS A 128 ALA A 133 1 6 HELIX 6 6 GLY A 135 ALA A 141 1 7 HELIX 7 7 ASP A 151 GLY A 163 1 13 HELIX 8 8 SER A 185 GLU A 190 1 6 HELIX 9 9 THR A 193 ALA A 197 1 5 HELIX 10 10 PRO A 207 ALA A 214 1 8 HELIX 11 11 LEU A 216 PHE A 230 1 15 HELIX 12 12 MET A 267 LEU A 275 1 9 HELIX 13 13 PRO A 307 ALA A 318 1 12 HELIX 14 14 CYS A 321 LEU A 338 1 18 HELIX 15 15 GLY A 343 ALA A 357 1 15 HELIX 16 16 VAL A 368 SER A 387 1 20 HELIX 17 17 GLY B 22 ASP B 34 1 13 HELIX 18 18 LEU B 51 THR B 61 1 11 HELIX 19 19 ASP B 86 GLN B 94 1 9 HELIX 20 20 LEU B 108 LYS B 118 1 11 HELIX 21 21 LYS B 128 ALA B 133 1 6 HELIX 22 22 GLY B 135 ALA B 141 1 7 HELIX 23 23 ASP B 151 GLY B 163 1 13 HELIX 24 24 SER B 185 GLU B 190 1 6 HELIX 25 25 THR B 193 ALA B 197 1 5 HELIX 26 26 GLY B 206 ALA B 214 1 9 HELIX 27 27 LEU B 216 PHE B 230 1 15 HELIX 28 28 MET B 267 LEU B 275 1 9 HELIX 29 29 PRO B 307 ALA B 318 1 12 HELIX 30 30 CYS B 321 LEU B 338 1 18 HELIX 31 31 GLY B 343 ALA B 357 1 15 HELIX 32 32 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 A1390 1555 1555 2.49 LINK OE1 GLU A 153 MN MN A1390 1555 1555 2.21 LINK OE2 GLU A 222 MN MN A1390 1555 1555 2.17 LINK MN MN A1390 O HOH A2166 1555 1555 2.21 LINK MN MN A1390 O HOH A2167 1555 1555 2.20 LINK MN MN A1390 O HOH A2168 1555 1555 2.21 LINK OD2 ASP B 151 MN MN B1390 1555 1555 2.19 LINK OE1 GLU B 153 MN MN B1390 1555 1555 2.21 LINK OE2 GLU B 222 MN MN B1390 1555 1555 2.18 LINK MN MN B1390 O HOH B2303 1555 1555 2.21 LINK MN MN B1390 O HOH B2304 1555 1555 2.19 LINK MN MN B1390 O HOH B2305 1555 1555 2.21 CISPEP 1 TRP A 277 PRO A 278 0 3.44 CISPEP 2 TRP B 277 PRO B 278 0 4.93 SITE 1 AC1 6 ASP A 151 GLU A 153 GLU A 222 HOH A2166 SITE 2 AC1 6 HOH A2167 HOH A2168 SITE 1 AC2 6 ASP B 151 GLU B 153 GLU B 222 HOH B2303 SITE 2 AC2 6 HOH B2304 HOH B2305 CRYST1 69.826 67.477 84.621 90.00 107.48 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 0.014321 0.000000 0.004510 0.00000 SCALE2 0.000000 0.014820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012390 0.00000 MTRIX1 1 0.236100 0.238900 -0.941900 36.20340 1 MTRIX2 1 0.223900 -0.956600 -0.186500 -3.86790 1 MTRIX3 1 -0.945600 -0.166900 -0.279300 46.76940 1