HEADER OXIDOREDUCTASE 25-OCT-16 5M6K TITLE CRYSTAL STRUCTURE OF NITROPHORIN 7 E27V MUTANT FROM RHODNIUS PROLIXUS TITLE 2 WITH IMIDAZOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROPHORIN-7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NP7,NITRITE DISMUTASE; COMPND 5 EC: 1.7.6.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODNIUS PROLIXUS; SOURCE 3 ORGANISM_TAXID: 13249; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NO TRANSPORTER, HEME PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.OGATA REVDAT 3 17-JAN-24 5M6K 1 REMARK REVDAT 2 22-AUG-18 5M6K 1 JRNL REVDAT 1 20-DEC-17 5M6K 0 JRNL AUTH S.ABBRUZZETTI,A.ALLEGRI,A.BIDON-CHANAL,H.OGATA,G.SOAVI, JRNL AUTH 2 G.CERULLO,S.BRUNO,C.MONTALI,F.J.LUQUE,C.VIAPPIANI JRNL TITL ELECTROSTATIC TUNING OF THE LIGAND BINDING MECHANISM BY JRNL TITL 2 GLU27 IN NITROPHORIN 7. JRNL REF SCI REP V. 8 10855 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 30022039 JRNL DOI 10.1038/S41598-018-29182-3 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 2011_08_24_1020 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 22579 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1128 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 23.8610 - 3.1978 1.00 2750 144 0.1496 0.1673 REMARK 3 2 3.1978 - 2.5391 1.00 2713 143 0.1562 0.2127 REMARK 3 3 2.5391 - 2.2184 1.00 2707 143 0.1521 0.2215 REMARK 3 4 2.2184 - 2.0157 1.00 2694 141 0.1382 0.2269 REMARK 3 5 2.0157 - 1.8713 1.00 2718 143 0.1480 0.2395 REMARK 3 6 1.8713 - 1.7610 1.00 2680 142 0.1790 0.2549 REMARK 3 7 1.7610 - 1.6728 1.00 2672 140 0.2075 0.2570 REMARK 3 8 1.6728 - 1.6000 0.93 2508 132 0.2535 0.3401 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 42.50 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.580 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) : 6.00650 REMARK 3 B22 (A**2) : -3.74570 REMARK 3 B33 (A**2) : -0.81440 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.60030 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 : 0.006 1566 REMARK 3 ANGLE : 1.075 2121 REMARK 3 CHIRALITY : 0.079 223 REMARK 3 PLANARITY : 0.004 263 REMARK 3 DIHEDRAL : 13.884 571 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 5M6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200002021. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83100 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.58100 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: 4XMC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NAOAC/HOAC, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K 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 33.32250 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 ALA A 82 24.43 -142.29 REMARK 500 LYS A 116 -122.09 50.28 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 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 60 NE2 REMARK 620 2 HEM A 201 NA 90.6 REMARK 620 3 HEM A 201 NB 94.1 89.1 REMARK 620 4 HEM A 201 NC 85.8 176.1 89.5 REMARK 620 5 HEM A 201 ND 84.8 90.9 178.9 90.4 REMARK 620 6 IMD A 202 N1 174.1 92.5 91.0 91.2 90.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 202 DBREF 5M6K A 2 185 UNP Q6PQK2 NP7_RHOPR 22 205 SEQADV 5M6K VAL A 27 UNP Q6PQK2 GLU 47 VARIANT SEQRES 1 A 184 PRO GLY GLU CYS SER VAL ASN VAL ILE PRO LYS LYS ASN SEQRES 2 A 184 LEU ASP LYS ALA LYS PHE PHE SER GLY THR TRP TYR VAL SEQRES 3 A 184 THR HIS TYR LEU ASP MET ASP PRO GLN ALA THR GLU LYS SEQRES 4 A 184 PHE CYS PHE SER PHE ALA PRO ARG GLU SER GLY GLY THR SEQRES 5 A 184 VAL LYS GLU ALA LEU TYR HIS PHE ASN VAL ASP SER LYS SEQRES 6 A 184 VAL SER PHE TYR ASN THR GLY THR GLY PRO LEU GLU SER SEQRES 7 A 184 ASN GLY ALA LYS TYR THR ALA LYS PHE ASN THR VAL ASP SEQRES 8 A 184 LYS LYS GLY LYS GLU ILE LYS PRO ALA ASP GLU LYS TYR SEQRES 9 A 184 SER TYR THR VAL THR VAL ILE GLU ALA ALA LYS GLN SER SEQRES 10 A 184 ALA LEU ILE HIS ILE CYS LEU GLN GLU ASP GLY LYS ASP SEQRES 11 A 184 ILE GLY ASP LEU TYR SER VAL LEU ASN ARG ASN LYS ASN SEQRES 12 A 184 ALA LEU PRO ASN LYS LYS ILE LYS LYS ALA LEU ASN LYS SEQRES 13 A 184 VAL SER LEU VAL LEU THR LYS PHE VAL VAL THR LYS ASP SEQRES 14 A 184 LEU ASP CYS LYS TYR ASP ASP LYS PHE LEU SER SER TRP SEQRES 15 A 184 GLN LYS HET HEM A 201 43 HET IMD A 202 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM IMD IMIDAZOLE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 IMD C3 H5 N2 1+ FORMUL 4 HOH *121(H2 O) HELIX 1 AA1 ASP A 16 PHE A 21 1 6 HELIX 2 AA2 ASN A 148 VAL A 158 1 11 HELIX 3 AA3 VAL A 161 PHE A 165 5 5 HELIX 4 AA4 LYS A 169 LEU A 171 5 3 HELIX 5 AA5 ASP A 176 SER A 182 1 7 SHEET 1 AA1 7 GLU A 97 LYS A 99 0 SHEET 2 AA1 7 LYS A 83 VAL A 91 -1 N THR A 90 O ILE A 98 SHEET 3 AA1 7 VAL A 67 PRO A 76 -1 N THR A 74 O LYS A 87 SHEET 4 AA1 7 THR A 53 ASN A 62 -1 N VAL A 54 O GLY A 75 SHEET 5 AA1 7 PHE A 41 SER A 50 -1 N CYS A 42 O PHE A 61 SHEET 6 AA1 7 TRP A 25 ASP A 32 -1 N TRP A 25 O PHE A 45 SHEET 7 AA1 7 VAL A 166 VAL A 167 -1 O VAL A 166 N TYR A 30 SHEET 1 AA2 7 GLU A 97 LYS A 99 0 SHEET 2 AA2 7 LYS A 83 VAL A 91 -1 N THR A 90 O ILE A 98 SHEET 3 AA2 7 TYR A 105 ALA A 115 -1 O VAL A 109 N TYR A 84 SHEET 4 AA2 7 SER A 118 GLU A 127 -1 O GLN A 126 N SER A 106 SHEET 5 AA2 7 LYS A 130 ASN A 140 -1 O GLY A 133 N LEU A 125 SHEET 6 AA2 7 TRP A 25 ASP A 32 -1 N HIS A 29 O VAL A 138 SHEET 7 AA2 7 VAL A 166 VAL A 167 -1 O VAL A 166 N TYR A 30 SSBOND 1 CYS A 5 CYS A 124 1555 1555 2.03 SSBOND 2 CYS A 42 CYS A 173 1555 1555 2.01 LINK NE2 HIS A 60 FE HEM A 201 1555 1555 2.27 LINK FE HEM A 201 N1 IMD A 202 1555 1555 2.04 SITE 1 AC1 14 VAL A 27 TYR A 30 PHE A 41 PHE A 43 SITE 2 AC1 14 GLU A 56 HIS A 60 ASN A 71 PHE A 88 SITE 3 AC1 14 TYR A 107 ILE A 123 LEU A 135 IMD A 202 SITE 4 AC1 14 HOH A 333 HOH A 335 SITE 1 AC2 4 ILE A 123 LEU A 125 HEM A 201 HOH A 331 CRYST1 38.260 66.645 38.494 90.00 116.72 90.00 P 1 21 1 2 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 0.026137 0.000000 0.013155 0.00000 SCALE2 0.000000 0.015005 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029083 0.00000