HEADER TRANSPORT PROTEIN 14-JAN-15 4XMH TITLE CRYSTAL STRUCTURE OF NITROPHORIN 7 FROM RHODNIUS PROLIXUS AT PH 7.8 TITLE 2 COMPLEXED WITH GLY-GLY-GLY COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROPHORIN-7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 21-205; COMPND 5 SYNONYM: NP7,NITRITE DISMUTASE; COMPND 6 EC: 1.7.6.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: GLY-GLY-GLY; COMPND 10 CHAIN: B; COMPND 11 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; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS HEME, NO TRANSPORTER, OXIDOREDUCTASE, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.OGATA REVDAT 2 10-JAN-24 4XMH 1 JRNL LINK REVDAT 1 29-JUL-15 4XMH 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) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.5 REMARK 3 NUMBER OF REFLECTIONS : 41069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 3737 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 34.7238 - 3.8674 0.97 2958 159 0.1644 0.1742 REMARK 3 2 3.8674 - 3.0702 0.95 2932 160 0.1569 0.1907 REMARK 3 3 3.0702 - 2.6823 0.98 2967 156 0.1787 0.1851 REMARK 3 4 2.6823 - 2.4371 0.98 2993 159 0.1709 0.2020 REMARK 3 5 2.4371 - 2.2625 0.96 2925 156 0.1548 0.1878 REMARK 3 6 2.2625 - 2.1291 0.97 2935 153 0.1483 0.1918 REMARK 3 7 2.1291 - 2.0225 0.97 2952 154 0.1459 0.1785 REMARK 3 8 2.0225 - 1.9345 0.96 2966 156 0.1374 0.1448 REMARK 3 9 1.9345 - 1.8600 0.95 2906 150 0.1284 0.1520 REMARK 3 10 1.8600 - 1.7958 0.95 2924 152 0.1294 0.1616 REMARK 3 11 1.7958 - 1.7397 0.95 2922 150 0.1239 0.1735 REMARK 3 12 1.7397 - 1.6899 0.95 2874 154 0.1191 0.1387 REMARK 3 13 1.6899 - 1.6454 0.95 2937 153 0.1125 0.1633 REMARK 3 14 1.6454 - 1.6053 0.95 2877 152 0.1173 0.1858 REMARK 3 15 1.6053 - 1.5688 0.93 2844 152 0.1276 0.1430 REMARK 3 16 1.5688 - 1.5354 0.93 2852 147 0.1325 0.1710 REMARK 3 17 1.5354 - 1.5047 0.93 2837 146 0.1299 0.1847 REMARK 3 18 1.5047 - 1.4763 0.92 2839 151 0.1379 0.1897 REMARK 3 19 1.4763 - 1.4499 0.91 2779 145 0.1442 0.2013 REMARK 3 20 1.4499 - 1.4254 0.90 2743 146 0.1589 0.1738 REMARK 3 21 1.4254 - 1.4024 0.86 2636 147 0.1810 0.2051 REMARK 3 22 1.4024 - 1.3808 0.76 2354 128 0.1903 0.2263 REMARK 3 23 1.3808 - 1.3605 0.70 2151 115 0.2014 0.2496 REMARK 3 24 1.3605 - 1.3413 0.64 1944 109 0.2097 0.2503 REMARK 3 25 1.3413 - 1.3232 0.56 1745 92 0.2277 0.3133 REMARK 3 26 1.3232 - 1.3060 0.43 1312 66 0.2564 0.3245 REMARK 3 27 1.3060 - 1.2897 0.18 544 29 0.3196 0.2947 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 44.88 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.670 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) : 5.51210 REMARK 3 B22 (A**2) : -4.49860 REMARK 3 B33 (A**2) : -3.70170 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.01290 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 1581 REMARK 3 ANGLE : 1.067 2138 REMARK 3 CHIRALITY : 0.084 223 REMARK 3 PLANARITY : 0.005 266 REMARK 3 DIHEDRAL : 13.659 578 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 4XMH 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_1000205940. 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 : 41095 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 (%) : 92.8 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.02400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 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) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 41.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 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 33.46450 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: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 23.53 -142.10 REMARK 500 LYS A 116 -121.59 53.45 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 89.2 REMARK 620 3 HEM A 201 NB 91.6 89.8 REMARK 620 4 HEM A 201 NC 91.5 178.3 88.5 REMARK 620 5 HEM A 201 ND 90.5 91.1 177.7 90.5 REMARK 620 6 GLY B 1 N 174.9 89.6 93.3 89.9 84.6 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 GOL A 202 DBREF 4XMH A 1 185 UNP Q6PQK2 NP7_RHOPR 21 205 DBREF 4XMH B 1 3 PDB 4XMH 4XMH 1 3 SEQRES 1 A 185 LEU PRO GLY GLU CYS SER VAL ASN VAL ILE PRO LYS LYS SEQRES 2 A 185 ASN LEU ASP LYS ALA LYS PHE PHE SER GLY THR TRP TYR SEQRES 3 A 185 GLU THR HIS TYR LEU ASP MET ASP PRO GLN ALA THR GLU SEQRES 4 A 185 LYS PHE CYS PHE SER PHE ALA PRO ARG GLU SER GLY GLY SEQRES 5 A 185 THR VAL LYS GLU ALA LEU TYR HIS PHE ASN VAL ASP SER SEQRES 6 A 185 LYS VAL SER PHE TYR ASN THR GLY THR GLY PRO LEU GLU SEQRES 7 A 185 SER ASN GLY ALA LYS TYR THR ALA LYS PHE ASN THR VAL SEQRES 8 A 185 ASP LYS LYS GLY LYS GLU ILE LYS PRO ALA ASP GLU LYS SEQRES 9 A 185 TYR SER TYR THR VAL THR VAL ILE GLU ALA ALA LYS GLN SEQRES 10 A 185 SER ALA LEU ILE HIS ILE CYS LEU GLN GLU ASP GLY LYS SEQRES 11 A 185 ASP ILE GLY ASP LEU TYR SER VAL LEU ASN ARG ASN LYS SEQRES 12 A 185 ASN ALA LEU PRO ASN LYS LYS ILE LYS LYS ALA LEU ASN SEQRES 13 A 185 LYS VAL SER LEU VAL LEU THR LYS PHE VAL VAL THR LYS SEQRES 14 A 185 ASP LEU ASP CYS LYS TYR ASP ASP LYS PHE LEU SER SER SEQRES 15 A 185 TRP GLN LYS SEQRES 1 B 3 GLY GLY GLY HET HEM A 201 43 HET GOL A 202 6 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM GOL GLYCEROL HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *162(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 SER A 118 N ALA A 115 SHEET 5 AA2 7 LYS A 130 ASN A 140 -1 O LEU A 139 N ALA A 119 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 2.03 SSBOND 2 CYS A 42 CYS A 173 1555 1555 2.03 LINK NE2 HIS A 60 FE HEM A 201 1555 1555 2.17 LINK FE HEM A 201 N GLY B 1 1555 1555 2.00 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 SER A 137 SITE 5 AC1 20 HOH A 316 HOH A 432 GLY B 1 HOH B 106 SITE 1 AC2 7 THR A 72 GLY A 73 THR A 74 LYS A 87 SITE 2 AC2 7 ASN A 89 ALA A 101 HOH A 306 CRYST1 38.374 66.929 38.885 90.00 116.79 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 0.026059 0.000000 0.013158 0.00000 SCALE2 0.000000 0.014941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028809 0.00000