HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 28-MAR-11 3RAS TITLE CRYSTAL STRUCTURE OF 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE TITLE 2 (DXR) COMPLEXED WITH A LIPOPHILIC PHOSPHONATE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP 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: 1773; SOURCE 4 GENE: DXR, RV2870C, MT2938, MTCY274.01C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, DOXP/MEP PATHWAY, ISOPRENE BIOSYNTHESIS, 1-DEOXY-D- KEYWDS 2 XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, OXIDOREDUCTASE-OXIDOREDUCTASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.DIAO,L.DENG,B.V.V.PRASAD,Y.SONG REVDAT 4 21-FEB-24 3RAS 1 REMARK SEQADV LINK REVDAT 3 25-JUL-12 3RAS 1 JRNL REVDAT 2 20-JUL-11 3RAS 1 HEADER REVDAT 1 25-MAY-11 3RAS 0 JRNL AUTH L.DENG,J.DIAO,P.CHEN,V.PUJARI,Y.YAO,G.CHENG,D.C.CRICK, JRNL AUTH 2 B.V.PRASAD,Y.SONG JRNL TITL INHIBITION OF 1-DEOXY-D-XYLULOSE-5-PHOSPHATE JRNL TITL 2 REDUCTOISOMERASE BY LIPOPHILIC PHOSPHONATES: SAR, QSAR, AND JRNL TITL 3 CRYSTALLOGRAPHIC STUDIES. JRNL REF J.MED.CHEM. V. 54 4721 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21561155 JRNL DOI 10.1021/JM200363D REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1308019.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 22333 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 SET) : 0.208 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1111 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3505 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE : 0.3740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 194 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 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 : 183 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 15.31000 REMARK 3 B22 (A**2) : 4.62000 REMARK 3 B33 (A**2) : -19.93000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.32000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.47 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.61 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.910 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.100 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.910 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.920 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 40.68 REMARK 3 REMARK 3 NCS MODEL : NONE REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NDP_PAR1.TXT REMARK 3 PARAMETER FILE 7 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NDP_TOP1.TXT REMARK 3 TOPOLOGY FILE 7 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3RAS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22365 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 33.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13600 REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.51800 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MTDXR (10 MG/ML) IN 20 MM TRIS, PH REMARK 280 7.5, 150 MM NACL, 2% GLYCEROL, 2 MM MNCL2, 3 MM NADPH WAS MIXED REMARK 280 WITH AN EQUAL VOLUME OF THE CRYSTALLIZATION BUFFER CONTAINING REMARK 280 0.2 M (NH4)2SO4, 25% POLYETHYLENE GLYCOL 3350, AND 0.1 M BIS- REMARK 280 TRIS, PH 5.7., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 32.58950 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: 6390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 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: 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 ARG A 12 132.83 -26.35 REMARK 500 ASN A 35 56.04 -149.36 REMARK 500 HIS A 50 69.66 -117.65 REMARK 500 ASN A 65 92.39 -68.12 REMARK 500 ASN A 127 84.69 -64.92 REMARK 500 PRO A 144 123.44 -37.67 REMARK 500 ASP A 167 2.70 -67.42 REMARK 500 PRO A 194 -18.14 -42.22 REMARK 500 SER A 249 156.78 158.40 REMARK 500 ASP A 266 98.59 -175.78 REMARK 500 TRP A 277 131.90 -38.26 REMARK 500 ALA A 293 153.21 -40.54 REMARK 500 ALA A 358 25.17 -70.86 REMARK 500 ASN B 35 56.03 -140.58 REMARK 500 LYS B 171 150.79 178.47 REMARK 500 ALA B 187 -71.04 -60.71 REMARK 500 ASP B 188 -39.17 -30.53 REMARK 500 ALA B 197 22.14 -68.46 REMARK 500 SER B 204 -66.07 -100.88 REMARK 500 SER B 249 161.57 175.01 REMARK 500 SER B 263 148.97 -173.52 REMARK 500 ASP B 266 113.90 -170.05 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 A 392 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 151 OD1 REMARK 620 2 GLU A 153 OE1 81.4 REMARK 620 3 GLU A 222 OE1 86.7 80.3 REMARK 620 4 FM5 A 390 O2 141.2 136.8 93.4 REMARK 620 5 FM5 A 390 O1 99.2 110.4 168.3 75.6 REMARK 620 6 DCV A 391 O2 121.0 154.9 89.3 20.5 79.0 REMARK 620 7 DCV A 391 O1 92.9 117.9 161.6 75.4 10.3 75.1 REMARK 620 8 DCV A 391 N1 128.9 143.0 117.3 25.2 51.2 30.1 50.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 392 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 151 OD1 REMARK 620 2 ASP B 151 OD2 50.5 REMARK 620 3 GLU B 153 OE1 100.6 104.2 REMARK 620 4 GLU B 222 OE1 113.3 70.5 63.3 REMARK 620 5 HOH B 462 O 87.3 135.9 95.1 151.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 1391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FM5 A 390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCV A 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 1392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FM5 B 390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCV B 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 393 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JCZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH FOSMIDOMYCIN, MANGANESE AND NADPH REMARK 900 RELATED ID: 2JCV RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH FOSMIDOMYCIN AND NADPH DBREF 3RAS A 2 389 UNP P64012 DXR_MYCTU 2 389 DBREF 3RAS B 2 389 UNP P64012 DXR_MYCTU 2 389 SEQADV 3RAS THR A -8 UNP P64012 EXPRESSION TAG SEQADV 3RAS MET A -7 UNP P64012 EXPRESSION TAG SEQADV 3RAS ALA A -6 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS A -5 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS A -4 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS A -3 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS A -2 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS A -1 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS A 0 UNP P64012 EXPRESSION TAG SEQADV 3RAS VAL A 1 UNP P64012 EXPRESSION TAG SEQADV 3RAS THR B -8 UNP P64012 EXPRESSION TAG SEQADV 3RAS MET B -7 UNP P64012 EXPRESSION TAG SEQADV 3RAS ALA B -6 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS B -5 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS B -4 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS B -3 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS B -2 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS B -1 UNP P64012 EXPRESSION TAG SEQADV 3RAS HIS B 0 UNP P64012 EXPRESSION TAG SEQADV 3RAS VAL B 1 UNP P64012 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 NDP A1391 48 HET FM5 A 390 20 HET DCV A 391 20 HET MN A 392 1 HET NDP B1392 48 HET FM5 B 390 20 HET DCV B 391 20 HET MN B 392 1 HET SO4 B 393 5 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM FM5 3-(N-HYDROXYACETAMIDO)-1-(3,4-DICHLOROPHENYL) HETNAM 2 FM5 PROPYLPHOSPHONIC ACID HETNAM DCV [(1R)-3-[ACETYL(HYDROXY)AMINO]-1-(3,4-DICHLOROPHENYL) HETNAM 2 DCV PROPYL]PHOSPHONIC ACID HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION FORMUL 3 NDP 2(C21 H30 N7 O17 P3) FORMUL 4 FM5 2(C11 H14 CL2 N O5 P) FORMUL 5 DCV 2(C11 H14 CL2 N O5 P) FORMUL 6 MN 2(MN 2+) FORMUL 11 SO4 O4 S 2- FORMUL 12 HOH *119(H2 O) HELIX 1 1 GLY A 22 ASP A 34 1 13 HELIX 2 2 HIS A 50 GLY A 62 1 13 HELIX 3 3 ASP A 70 GLY A 78 1 9 HELIX 4 4 ASP A 86 THR A 95 1 10 HELIX 5 5 GLY A 106 LEU A 108 5 3 HELIX 6 6 GLY A 109 GLY A 120 1 12 HELIX 7 7 ASN A 127 GLY A 135 1 9 HELIX 8 8 GLY A 135 ALA A 142 1 8 HELIX 9 9 ASP A 151 ARG A 162 1 12 HELIX 10 10 GLY A 163 GLY A 164 5 2 HELIX 11 11 THR A 165 ASP A 167 5 3 HELIX 12 12 SER A 185 GLU A 190 1 6 HELIX 13 13 GLY A 206 SER A 215 1 10 HELIX 14 14 LEU A 216 GLY A 231 1 16 HELIX 15 15 PRO A 233 ASP A 235 5 3 HELIX 16 16 MET A 267 TRP A 277 1 11 HELIX 17 17 PRO A 307 GLY A 319 1 13 HELIX 18 18 CYS A 321 ALA A 339 1 19 HELIX 19 19 PHE A 344 ALA A 358 1 15 HELIX 20 20 ASP A 359 ALA A 362 5 4 HELIX 21 21 THR A 367 SER A 387 1 21 HELIX 22 22 GLY B 22 ASP B 34 1 13 HELIX 23 23 HIS B 50 GLY B 62 1 13 HELIX 24 24 ASP B 70 ARG B 76 1 7 HELIX 25 25 ASP B 86 THR B 95 1 10 HELIX 26 26 GLY B 106 LEU B 108 5 3 HELIX 27 27 GLY B 109 THR B 119 1 11 HELIX 28 28 ASN B 127 ALA B 133 1 7 HELIX 29 29 GLY B 134 ALA B 142 1 9 HELIX 30 30 ASP B 151 LEU B 161 1 11 HELIX 31 31 ARG B 162 GLY B 164 5 3 HELIX 32 32 THR B 165 ASP B 167 5 3 HELIX 33 33 ALA B 187 VAL B 192 5 6 HELIX 34 34 GLY B 206 SER B 215 1 10 HELIX 35 35 LEU B 216 GLY B 231 1 16 HELIX 36 36 PRO B 233 ASP B 235 5 3 HELIX 37 37 MET B 267 TRP B 277 1 11 HELIX 38 38 PRO B 307 GLY B 319 1 13 HELIX 39 39 CYS B 321 ALA B 339 1 19 HELIX 40 40 PRO B 345 ALA B 357 1 13 HELIX 41 41 ALA B 358 VAL B 363 5 6 HELIX 42 42 THR B 367 GLY B 388 1 22 SHEET 1 A 7 TYR A 82 HIS A 83 0 SHEET 2 A 7 ILE A 66 VAL A 68 1 N VAL A 68 O TYR A 82 SHEET 3 A 7 PHE A 39 ALA A 46 1 N LEU A 44 O ALA A 67 SHEET 4 A 7 LEU A 13 LEU A 18 1 N VAL A 17 O GLY A 43 SHEET 5 A 7 VAL A 99 ASN A 102 1 O LEU A 101 N VAL A 16 SHEET 6 A 7 ARG A 122 LEU A 125 1 O ALA A 124 N ASN A 102 SHEET 7 A 7 ILE A 147 PRO A 149 1 O VAL A 148 N LEU A 125 SHEET 1 B 4 ILE A 237 VAL A 241 0 SHEET 2 B 4 VAL A 169 ALA A 176 1 N LEU A 172 O ASP A 238 SHEET 3 B 4 ILE A 247 PHE A 253 -1 O THR A 252 N ALA A 170 SHEET 4 B 4 THR A 258 ALA A 262 -1 O GLN A 261 N HIS A 248 SHEET 1 C 7 TYR B 82 HIS B 83 0 SHEET 2 C 7 ILE B 66 VAL B 68 1 N VAL B 68 O TYR B 82 SHEET 3 C 7 PHE B 39 ALA B 46 1 N ALA B 46 O ALA B 67 SHEET 4 C 7 LEU B 13 LEU B 18 1 N VAL B 15 O GLU B 40 SHEET 5 C 7 VAL B 99 ASN B 102 1 O LEU B 101 N VAL B 16 SHEET 6 C 7 ARG B 122 LEU B 125 1 O ARG B 122 N VAL B 100 SHEET 7 C 7 ILE B 147 PRO B 149 1 O VAL B 148 N LEU B 123 SHEET 1 D 4 ILE B 237 VAL B 241 0 SHEET 2 D 4 VAL B 169 ALA B 176 1 N LEU B 174 O ASP B 238 SHEET 3 D 4 ILE B 247 PHE B 253 -1 O MET B 250 N VAL B 173 SHEET 4 D 4 THR B 258 ALA B 262 -1 O ILE B 259 N VAL B 251 LINK OD1 ASP A 151 MN MN A 392 1555 1555 2.02 LINK OE1 GLU A 153 MN MN A 392 1555 1555 2.01 LINK OE1 GLU A 222 MN MN A 392 1555 1555 2.08 LINK O2 FM5 A 390 MN MN A 392 1555 1555 2.19 LINK O1 FM5 A 390 MN MN A 392 1555 1555 2.30 LINK O2 DCV A 391 MN MN A 392 1555 1555 2.04 LINK O1 DCV A 391 MN MN A 392 1555 1555 2.51 LINK N1 DCV A 391 MN MN A 392 1555 1555 2.76 LINK OD1 ASP B 151 MN MN B 392 1555 1555 2.21 LINK OD2 ASP B 151 MN MN B 392 1555 1555 2.80 LINK OE1 GLU B 153 MN MN B 392 1555 1555 2.59 LINK OE1 GLU B 222 MN MN B 392 1555 1555 2.04 LINK MN MN B 392 O HOH B 462 1555 1555 2.51 CISPEP 1 TRP A 277 PRO A 278 0 -0.25 CISPEP 2 TRP B 277 PRO B 278 0 0.05 SITE 1 AC1 27 GLY A 19 THR A 21 GLY A 22 SER A 23 SITE 2 AC1 27 ILE A 24 ALA A 46 GLY A 47 GLY A 48 SITE 3 AC1 27 ALA A 49 HIS A 50 ALA A 69 ALA A 103 SITE 4 AC1 27 LEU A 104 LEU A 108 ALA A 126 ASN A 127 SITE 5 AC1 27 LYS A 128 GLU A 129 ASP A 151 MET A 205 SITE 6 AC1 27 GLY A 206 PRO A 207 ASN A 209 MET A 267 SITE 7 AC1 27 FM5 A 390 DCV A 391 HOH A 399 SITE 1 AC2 16 ASP A 151 SER A 152 GLU A 153 ALA A 176 SITE 2 AC2 16 SER A 177 TRP A 203 MET A 205 ASN A 209 SITE 3 AC2 16 SER A 213 ASN A 218 LYS A 219 GLU A 222 SITE 4 AC2 16 SER A 245 DCV A 391 MN A 392 NDP A1391 SITE 1 AC3 16 LYS A 128 ASP A 151 SER A 152 ALA A 176 SITE 2 AC3 16 SER A 177 TRP A 203 MET A 205 ASN A 209 SITE 3 AC3 16 SER A 213 ASN A 218 LYS A 219 GLU A 222 SITE 4 AC3 16 SER A 245 FM5 A 390 MN A 392 NDP A1391 SITE 1 AC4 23 GLY B 19 THR B 21 GLY B 22 SER B 23 SITE 2 AC4 23 ILE B 24 ALA B 46 GLY B 47 GLY B 48 SITE 3 AC4 23 ALA B 49 HIS B 50 ALA B 69 ALA B 103 SITE 4 AC4 23 LEU B 104 LEU B 108 ALA B 126 ASN B 127 SITE 5 AC4 23 LYS B 128 ASP B 151 MET B 267 HOH B 397 SITE 6 AC4 23 HOH B 422 HOH B 423 HOH B 434 SITE 1 AC5 5 ASP A 151 GLU A 153 GLU A 222 FM5 A 390 SITE 2 AC5 5 DCV A 391 SITE 1 AC6 6 THR B 21 HIS B 50 THR B 53 TRP B 203 SITE 2 AC6 6 DCV B 391 HOH B 412 SITE 1 AC7 6 HIS B 50 THR B 53 TRP B 203 FM5 B 390 SITE 2 AC7 6 HOH B 395 HOH B 412 SITE 1 AC8 4 ASP B 151 GLU B 153 GLU B 222 HOH B 462 SITE 1 AC9 6 ALA B 176 SER B 177 SER B 213 ASN B 218 SITE 2 AC9 6 LYS B 219 HOH B 444 CRYST1 67.250 65.179 85.408 90.00 101.28 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 0.014870 0.000000 0.002966 0.00000 SCALE2 0.000000 0.015342 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011939 0.00000