HEADER OXIDOREDUCTASE 08-APR-15 4Z85 TITLE CRYSTAL STRUCTUR OF PSEUDOMONAS FLUORESCENS 2-NITROBENZOATE 2- TITLE 2 NITROREDUCTASE NBAA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-NITROBENZOATE NITROREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS FLUORESCENS; SOURCE 3 ORGANISM_TAXID: 294; SOURCE 4 GENE: NBAA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS 2-NITROBENZOATE 2-NITROREDUCTASE (NBAA), 2-NITROBENZOATE METHYL KEYWDS 2 ESTER, FMN-BINDING SITE, TYROSINE MODIFICATION, CYSTEINE REACTIVITY, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.C.HA,L.JIAO,J.S.KIM REVDAT 2 08-NOV-23 4Z85 1 JRNL REMARK REVDAT 1 20-JAN-16 4Z85 0 JRNL AUTH Y.H.KIM,W.SONG,J.S.KIM,L.JIAO,K.LEE,N.C.HA JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO THE PSEUDOMONAS JRNL TITL 2 FLUORESCENS 2-NITROBENZOATE 2-NITROREDUCTASE NBAA JRNL REF APPL.ENVIRON.MICROBIOL. V. 81 5266 2015 JRNL REFN ESSN 1098-5336 JRNL PMID 26025888 JRNL DOI 10.1128/AEM.01289-15 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 24861 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1264 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 19.0960 - 3.5296 0.97 2609 135 0.1588 0.1726 REMARK 3 2 3.5296 - 2.8044 1.00 2654 135 0.1859 0.2142 REMARK 3 3 2.8044 - 2.4507 1.00 2620 150 0.2009 0.2464 REMARK 3 4 2.4507 - 2.2270 1.00 2610 157 0.1983 0.2127 REMARK 3 5 2.2270 - 2.0676 1.00 2614 154 0.2088 0.2398 REMARK 3 6 2.0676 - 1.9458 1.00 2630 129 0.2116 0.2467 REMARK 3 7 1.9458 - 1.8485 1.00 2623 123 0.2227 0.2656 REMARK 3 8 1.8485 - 1.7681 1.00 2615 151 0.2245 0.3037 REMARK 3 9 1.7681 - 1.7000 1.00 2622 130 0.2242 0.2666 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.007 1596 REMARK 3 ANGLE : 1.097 2166 REMARK 3 CHIRALITY : 0.044 247 REMARK 3 PLANARITY : 0.005 279 REMARK 3 DIHEDRAL : 12.949 594 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 4Z85 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208796. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97188 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24944 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 21.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 92.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: 1EJE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE (PH 4.6), 1 MM REMARK 280 FMN, 1 MM MNCL2, 30% V/V PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,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 26.80400 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 53.60800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.80400 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 53.60800 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: 9000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -35.25400 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 61.06172 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 TYR A 64 REMARK 465 GLY A 65 REMARK 465 GLU A 66 REMARK 465 GLU A 67 REMARK 465 SER A 68 REMARK 465 HIS A 69 REMARK 465 ARG A 70 REMARK 465 PRO A 71 REMARK 465 GLY A 72 REMARK 465 GLU A 73 REMARK 465 GLN A 74 REMARK 465 PRO A 108 REMARK 465 SER A 109 REMARK 465 HIS A 110 REMARK 465 LYS A 213 REMARK 465 PRO A 214 REMARK 465 ARG A 215 REMARK 465 GLU A 216 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 CYS A 194 SG 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 A 327 O HOH A 337 1.93 REMARK 500 O HOH A 337 O HOH A 364 2.02 REMARK 500 O HOH A 370 O HOH A 393 2.06 REMARK 500 O HOH A 337 O HOH A 339 2.10 REMARK 500 O HOH A 360 O HOH A 401 2.11 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 ASP A 93 -169.15 -126.07 REMARK 500 PRO A 191 45.73 -84.12 REMARK 500 THR A 196 56.18 -93.72 REMARK 500 REMARK 500 REMARK: NULL DBREF 4Z85 A 1 216 UNP A4UVY1 A4UVY1_PSEFL 1 216 SEQRES 1 A 216 MET THR HIS ILE ALA MET SER GLY LEU THR ASN MET GLN SEQRES 2 A 216 LYS TYR TRP LEU ILE THR GLY SER VAL GLY PRO ARG PRO SEQRES 3 A 216 ILE ALA LEU VAL THR SER LEU ASN SER GLU GLY LEU CYS SEQRES 4 A 216 ASN ALA ALA PRO TYR SER ALA PHE ASN TYR MET GLY GLU SEQRES 5 A 216 ASP PRO PRO LEU PHE VAL ILE ALA VAL ASP HIS TYR GLY SEQRES 6 A 216 GLU GLU SER HIS ARG PRO GLY GLU GLN LYS ASP THR LEU SEQRES 7 A 216 LYS ASN ILE ILE GLU ARG GLU GLN PHE VAL VAL ASN MET SEQRES 8 A 216 VAL ASP GLU ARG ILE ALA GLU ARG MET VAL LEU CYS GLY SEQRES 9 A 216 SER ASP PHE PRO SER HIS ILE SER GLU ALA GLU ALA VAL SEQRES 10 A 216 GLY PHE ASP LEU THR PRO SER THR THR ILE ASP VAL PRO SEQRES 11 A 216 ARG ILE THR ASP ALA PRO ILE ALA TRP GLU CYS LYS LEU SEQRES 12 A 216 TYR LYS ILE ILE ASP PHE SER LYS GLN ARG SER MET VAL SEQRES 13 A 216 PHE GLY GLU ILE VAL ALA MET TYR PHE ARG GLU GLU LEU SEQRES 14 A 216 ILE ASP GLU GLU LYS LEU ARG VAL ARG VAL ASP LEU PHE SEQRES 15 A 216 GLN PRO TYR GLY ARG LEU GLY GLY PRO ASN TYR CYS ARG SEQRES 16 A 216 THR THR ASP ARG VAL ARG LEU THR VAL PRO THR PHE LEU SEQRES 17 A 216 PRO SER ALA GLY LYS PRO ARG GLU FORMUL 2 HOH *111(H2 O) HELIX 1 AA1 ALA A 5 LEU A 9 5 5 HELIX 2 AA2 THR A 10 VAL A 22 1 13 HELIX 3 AA3 ASP A 76 GLU A 85 1 10 HELIX 4 AA4 ASP A 93 GLY A 104 1 12 HELIX 5 AA5 SER A 112 GLY A 118 1 7 SHEET 1 AA1 7 CYS A 39 TYR A 44 0 SHEET 2 AA1 7 ALA A 28 LEU A 33 -1 N ALA A 28 O TYR A 44 SHEET 3 AA1 7 GLN A 86 ASN A 90 -1 O ASN A 90 N LEU A 29 SHEET 4 AA1 7 ILE A 137 SER A 150 -1 O TRP A 139 N VAL A 89 SHEET 5 AA1 7 ARG A 153 PHE A 165 -1 O GLU A 159 N LYS A 142 SHEET 6 AA1 7 LEU A 56 ASP A 62 -1 N VAL A 61 O SER A 154 SHEET 7 AA1 7 PHE A 47 GLY A 51 -1 N MET A 50 O LEU A 56 SHEET 1 AA2 2 LEU A 121 THR A 122 0 SHEET 2 AA2 2 ARG A 131 ILE A 132 -1 O ARG A 131 N THR A 122 SHEET 1 AA3 2 ILE A 170 ASP A 171 0 SHEET 2 AA3 2 ARG A 176 VAL A 177 -1 O ARG A 176 N ASP A 171 SHEET 1 AA4 2 TYR A 185 ARG A 187 0 SHEET 2 AA4 2 TYR A 193 ARG A 195 -1 O CYS A 194 N GLY A 186 CISPEP 1 GLY A 23 PRO A 24 0 -8.59 CISPEP 2 ASP A 53 PRO A 54 0 -0.45 CRYST1 70.508 70.508 80.412 90.00 90.00 120.00 P 64 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 0.014183 0.008188 0.000000 0.00000 SCALE2 0.000000 0.016377 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012436 0.00000