HEADER OXIDOREDUCTASE 19-MAR-11 3R5P TITLE STRUCTURE OF DDN, THE DEAZAFLAVIN-DEPENDENT NITROREDUCTASE FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS INVOLVED IN BIOREDUCTIVE ACTIVATION OF PA- TITLE 3 824 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEAZAFLAVIN-DEPENDENT NITROREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.-.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: DDN, MT3651, RV3547; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PA-824, SPLIT BARREL-LIKE FOLD, DUF385, DEAZAFLAVIN-DEPENDENT KEYWDS 2 NITROREDUCTASE, NITROIMIDAZOLES, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.E.CELLITTI,J.SHAFFER,D.H.JONES,T.MUKHERJEE,M.GURUMURTHY, AUTHOR 2 B.BURSULAYA,H.I.M.BOSHOFF,I.CHOI,A.NAYYA,Y.S.LEE,J.CHERIAN, AUTHOR 3 P.NIYOMRATTANAKIT,T.DICK,U.H.MANJUNATHA,C.E.BARRY,G.SPRAGGON, AUTHOR 4 B.H.GEIERSTANGER REVDAT 5 06-DEC-23 3R5P 1 REMARK REVDAT 4 13-SEP-23 3R5P 1 REMARK LINK REVDAT 3 08-NOV-17 3R5P 1 REMARK REVDAT 2 21-MAR-12 3R5P 1 JRNL REVDAT 1 18-JAN-12 3R5P 0 JRNL AUTH S.E.CELLITTI,J.SHAFFER,D.H.JONES,T.MUKHERJEE,M.GURUMURTHY, JRNL AUTH 2 B.BURSULAYA,H.I.BOSHOFF,I.CHOI,A.NAYYAR,Y.S.LEE,J.CHERIAN, JRNL AUTH 3 P.NIYOMRATTANAKIT,T.DICK,U.H.MANJUNATHA,C.E.BARRY, JRNL AUTH 4 G.SPRAGGON,B.H.GEIERSTANGER JRNL TITL STRUCTURE OF DDN, THE DEAZAFLAVIN-DEPENDENT NITROREDUCTASE JRNL TITL 2 FROM MYCOBACTERIUM TUBERCULOSIS INVOLVED IN BIOREDUCTIVE JRNL TITL 3 ACTIVATION OF PA-824. JRNL REF STRUCTURE V. 20 101 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22244759 JRNL DOI 10.1016/J.STR.2011.11.001 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.5_2 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : CCP4 MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.160 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 14350 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 722 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 41.6560 - 3.1625 1.00 3039 151 0.1656 0.1831 REMARK 3 2 3.1625 - 2.5103 0.98 2927 140 0.1629 0.1900 REMARK 3 3 2.5103 - 2.1930 0.97 2825 153 0.1659 0.2111 REMARK 3 4 2.1930 - 1.9925 0.92 2646 160 0.1747 0.2243 REMARK 3 5 1.9925 - 1.8500 0.75 2191 118 0.2236 0.2752 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 52.48 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.17520 REMARK 3 B22 (A**2) : 3.17520 REMARK 3 B33 (A**2) : -6.35050 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.018 961 REMARK 3 ANGLE : 1.747 1315 REMARK 3 CHIRALITY : 0.136 145 REMARK 3 PLANARITY : 0.009 167 REMARK 3 DIHEDRAL : 18.227 365 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3R5P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064521. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15215 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.11300 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) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.57200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.214 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: PDB ENTRY 3R5L (PRELIMINARY MODEL USED FOR MR) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M (NH4)2SO4, 0.1M CITRIC ACID, PH REMARK 280 4.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.46933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.23467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 11.23467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.46933 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLY A 34 REMARK 465 GLU A 35 REMARK 465 GLY A 36 REMARK 465 LEU A 37 REMARK 465 GLY A 38 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 LYS A 103 -119.79 55.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3R5L RELATED DB: PDB REMARK 900 THE SAME PROTEIN CRYSTALLIZED IN A DIFFERENT SPACE GROUP REMARK 900 RELATED ID: 3R5R RELATED DB: PDB REMARK 900 SAME PROTEIN WITH CO-FACTOR REMARK 900 RELATED ID: 3R5W RELATED DB: PDB REMARK 900 SAME PROTEIN WITH CO-FACTOR REMARK 900 RELATED ID: 3R5Y RELATED DB: PDB REMARK 900 HOMOLOGOUS PROTEIN FROM N. FARCINICA REMARK 900 RELATED ID: 3R5Z RELATED DB: PDB REMARK 900 HOMOLOGOUS PROTEIN FROM N. FARCINICA DBREF 3R5P A 34 151 UNP P71854 DDN_MYCTU 34 151 SEQRES 1 A 118 GLY GLU GLY LEU GLY GLY THR PHE GLN LYS ILE PRO VAL SEQRES 2 A 118 ALA LEU LEU THR THR THR GLY ARG LYS THR GLY GLN PRO SEQRES 3 A 118 ARG VAL ASN PRO LEU TYR PHE LEU ARG ASP GLY GLY ARG SEQRES 4 A 118 VAL ILE VAL ALA ALA SER LYS GLY GLY ALA GLU LYS ASN SEQRES 5 A 118 PRO MSE TRP TYR LEU ASN LEU LYS ALA ASN PRO LYS VAL SEQRES 6 A 118 GLN VAL GLN ILE LYS LYS GLU VAL LEU ASP LEU THR ALA SEQRES 7 A 118 ARG ASP ALA THR ASP GLU GLU ARG ALA GLU TYR TRP PRO SEQRES 8 A 118 GLN LEU VAL THR MSE TYR PRO SER TYR GLN ASP TYR GLN SEQRES 9 A 118 SER TRP THR ASP ARG THR ILE PRO ILE VAL VAL CYS GLU SEQRES 10 A 118 PRO MODRES 3R5P MSE A 87 MET SELENOMETHIONINE MODRES 3R5P MSE A 129 MET SELENOMETHIONINE HET MSE A 87 8 HET MSE A 129 8 HET SO4 A 201 5 HET SO4 A 202 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *108(H2 O) HELIX 1 1 PRO A 86 ASN A 95 1 10 HELIX 2 2 THR A 115 TYR A 130 1 16 HELIX 3 3 PRO A 131 TYR A 136 5 6 HELIX 4 4 GLN A 137 THR A 143 1 7 SHEET 1 A 7 ALA A 47 THR A 52 0 SHEET 2 A 7 PRO A 59 ASP A 69 -1 O LEU A 64 N ALA A 47 SHEET 3 A 7 ARG A 72 ALA A 76 -1 O ILE A 74 N LEU A 67 SHEET 4 A 7 ILE A 146 GLU A 150 -1 O CYS A 149 N VAL A 73 SHEET 5 A 7 GLU A 105 ASP A 113 -1 N ARG A 112 O VAL A 148 SHEET 6 A 7 LYS A 97 ILE A 102 -1 N VAL A 100 O LEU A 107 SHEET 7 A 7 ALA A 47 THR A 52 -1 N THR A 50 O GLN A 99 LINK C PRO A 86 N MSE A 87 1555 1555 1.32 LINK C MSE A 87 N TRP A 88 1555 1555 1.34 LINK C THR A 128 N MSE A 129 1555 1555 1.32 LINK C MSE A 129 N TYR A 130 1555 1555 1.33 SITE 1 AC1 6 GLY A 53 ARG A 54 LYS A 55 THR A 56 SITE 2 AC1 6 ARG A 60 HOH A 403 SITE 1 AC2 4 ASN A 62 PRO A 86 MSE A 87 TRP A 88 CRYST1 96.176 96.176 33.704 90.00 90.00 120.00 P 32 2 1 6 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 0.010398 0.006003 0.000000 0.00000 SCALE2 0.000000 0.012006 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029670 0.00000