HEADER TRANSPORT PROTEIN 14-JAN-15 4XME TITLE CRYSTAL STRUCTURE OF NITROPHORIN 7 FROM RHODNIUS PROLIXUS AT PH 7.8 TITLE 2 COMPLEXED WITH NO COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROPHORIN-7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 22-205; COMPND 5 SYNONYM: NP7,NITRITE DISMUTASE; COMPND 6 EC: 1.7.6.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODNIUS PROLIXUS; SOURCE 3 ORGANISM_COMMON: TRIATOMID BUG; SOURCE 4 ORGANISM_TAXID: 13249; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEME, NO TRANSPORTER, OXIDOREDUCTASE, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.OGATA REVDAT 2 10-JAN-24 4XME 1 JRNL REVDAT 1 29-JUL-15 4XME 0 JRNL AUTH M.KNIPP,H.OGATA,G.SOAVI,G.CERULLO,A.ALLEGRI,S.ABBRUZZETTI, JRNL AUTH 2 S.BRUNO,C.VIAPPIANI,A.BIDON-CHANAL,F.J.LUQUE JRNL TITL STRUCTURE AND DYNAMICS OF THE MEMBRANE ATTACHING NITRIC JRNL TITL 2 OXIDE TRANSPORTER NITROPHORIN 7. JRNL REF F1000RES V. 4 45 2015 JRNL REFN ESSN 2046-1402 JRNL PMID 26167269 JRNL DOI 10.12688/F1000RESEARCH.6060.1 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 83819 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 4183 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 34.7268 - 3.9975 0.95 2698 140 0.1694 0.2108 REMARK 3 2 3.9975 - 3.1736 0.98 2752 140 0.1638 0.1906 REMARK 3 3 3.1736 - 2.7726 0.98 2729 145 0.1779 0.2058 REMARK 3 4 2.7726 - 2.5192 0.98 2803 150 0.1810 0.2322 REMARK 3 5 2.5192 - 2.3387 0.89 2506 132 0.1652 0.1939 REMARK 3 6 2.3387 - 2.2008 0.92 2612 139 0.1511 0.1733 REMARK 3 7 2.2008 - 2.0906 0.96 2668 141 0.1534 0.1690 REMARK 3 8 2.0906 - 1.9996 0.97 2755 143 0.1388 0.1846 REMARK 3 9 1.9996 - 1.9226 0.98 2773 146 0.1323 0.1868 REMARK 3 10 1.9226 - 1.8563 0.98 2728 144 0.1353 0.1957 REMARK 3 11 1.8563 - 1.7983 0.99 2821 153 0.1412 0.1585 REMARK 3 12 1.7983 - 1.7469 0.95 2664 142 0.1293 0.2056 REMARK 3 13 1.7469 - 1.7009 0.90 2503 132 0.1277 0.1441 REMARK 3 14 1.7009 - 1.6594 0.94 2671 143 0.1319 0.1592 REMARK 3 15 1.6594 - 1.6217 0.95 2632 137 0.1337 0.1928 REMARK 3 16 1.6217 - 1.5872 0.96 2771 144 0.1408 0.1880 REMARK 3 17 1.5872 - 1.5554 0.96 2669 137 0.1505 0.1714 REMARK 3 18 1.5554 - 1.5261 0.97 2799 144 0.1698 0.2001 REMARK 3 19 1.5261 - 1.4988 0.97 2683 139 0.1748 0.2185 REMARK 3 20 1.4988 - 1.4734 0.98 2788 148 0.1840 0.2337 REMARK 3 21 1.4734 - 1.4496 0.98 2709 143 0.1964 0.2412 REMARK 3 22 1.4496 - 1.4273 0.96 2756 147 0.2214 0.2650 REMARK 3 23 1.4273 - 1.4063 0.88 2461 126 0.2415 0.2578 REMARK 3 24 1.4063 - 1.3865 0.89 2459 134 0.2622 0.3038 REMARK 3 25 1.3865 - 1.3678 0.92 2639 138 0.2618 0.2928 REMARK 3 26 1.3678 - 1.3500 0.94 2575 134 0.2896 0.3113 REMARK 3 27 1.3500 - 1.3331 0.93 2673 137 0.3114 0.3164 REMARK 3 28 1.3331 - 1.3171 0.94 2685 139 0.3251 0.3628 REMARK 3 29 1.3171 - 1.3018 0.94 2587 139 0.3541 0.3387 REMARK 3 30 1.3018 - 1.2871 0.73 2067 107 0.4004 0.3906 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 56.62 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.490 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) : -2.72070 REMARK 3 B22 (A**2) : 1.10010 REMARK 3 B33 (A**2) : 1.62060 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.07780 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 : 0.010 1552 REMARK 3 ANGLE : 1.074 2098 REMARK 3 CHIRALITY : 0.085 220 REMARK 3 PLANARITY : 0.005 259 REMARK 3 DIHEDRAL : 12.898 566 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 4XME COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205933. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83829 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 34.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.92500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 3MVF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25%(W/V) PEG 3350, 0.1 M BIS-TRIS REMARK 280 PROPANE PH 7.8, 0.25%(W/V) GLY-GLY, 0.25%(W/V) GLY-GLY-GLY, 0.25% REMARK 280 (W/V) GLY- GLY-GLY-GLY, 0.25%(W/V) PENTAGLYCINE, 0.02 M HEPES REMARK 280 SODIUM PH 6.8., VAPOR DIFFUSION, SITTING 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 33.52600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 20.93 -140.12 REMARK 500 LYS A 116 -122.85 52.98 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 86.2 REMARK 620 3 HEM A 201 NB 90.9 89.4 REMARK 620 4 HEM A 201 NC 91.1 177.3 90.6 REMARK 620 5 HEM A 201 ND 89.3 89.7 179.1 90.3 REMARK 620 6 NO A 202 N 174.9 91.7 93.7 91.0 86.1 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 NO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 DBREF 4XME A 2 185 UNP Q6PQK2 NP7_RHOPR 22 205 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 GLU 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 NO A 202 2 HET GOL A 203 6 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NO NITRIC OXIDE HETNAM GOL GLYCEROL HETSYN HEM HEME HETSYN NO NITROGEN MONOXIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 NO N O FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *150(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 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 TYR A 107 N ALA A 86 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 THR A 28 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 2.04 SSBOND 2 CYS A 42 CYS A 173 1555 1555 2.03 LINK NE2 HIS A 60 FE HEM A 201 1555 1555 2.23 LINK FE HEM A 201 N NO A 202 1555 1555 1.79 SITE 1 AC1 20 GLU A 27 TYR A 30 PHE A 41 PHE A 43 SITE 2 AC1 20 GLU A 56 LEU A 58 HIS A 60 PHE A 69 SITE 3 AC1 20 ASN A 71 PHE A 88 THR A 90 TYR A 107 SITE 4 AC1 20 VAL A 109 ILE A 121 ILE A 123 LEU A 135 SITE 5 AC1 20 SER A 137 NO A 202 HOH A 335 HOH A 422 SITE 1 AC2 2 ILE A 123 HEM A 201 SITE 1 AC3 5 THR A 72 GLY A 73 THR A 74 LYS A 87 SITE 2 AC3 5 ASN A 89 CRYST1 38.887 67.052 39.082 90.00 117.35 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 0.025716 0.000000 0.013300 0.00000 SCALE2 0.000000 0.014914 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028807 0.00000