HEADER TRANSPORT PROTEIN 14-JAN-15 4XMD TITLE CRYSTAL STRUCTURE OF NITROPHORIN 7 FROM RHODNIUS PROLIXUS AT PH 7.8 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 TRANSPOTER, OXIDOREDUCTASE, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.OGATA REVDAT 2 10-JAN-24 4XMD 1 JRNL REVDAT 1 29-JUL-15 4XMD 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. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1565) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23137 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1158 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 30.4000 - 3.1989 1.00 2788 147 0.1253 0.1612 REMARK 3 2 3.1989 - 2.5395 1.00 2754 145 0.1413 0.2107 REMARK 3 3 2.5395 - 2.2186 1.00 2758 145 0.1342 0.1887 REMARK 3 4 2.2186 - 2.0158 1.00 2725 144 0.1276 0.1929 REMARK 3 5 2.0158 - 1.8713 1.00 2767 145 0.1248 0.1906 REMARK 3 6 1.8713 - 1.7610 1.00 2703 143 0.1435 0.2264 REMARK 3 7 1.7610 - 1.6728 1.00 2742 144 0.1531 0.2593 REMARK 3 8 1.6728 - 1.6000 1.00 2742 145 0.1888 0.2644 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.250 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 : 0.006 1553 REMARK 3 ANGLE : 1.026 2106 REMARK 3 CHIRALITY : 0.045 222 REMARK 3 PLANARITY : 0.004 261 REMARK 3 DIHEDRAL : 14.069 567 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 4XMD 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_1000205932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-11 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 : 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 : 23143 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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 (%): 42.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25%(W/V) PEG 3350, 0.1 M BIS-TRIS REMARK 280 PROPANE PH 7.8, 0.02 M HEPES PH 6.8, 0.25%(W/V) NAPHTHALENE-1,3, REMARK 280 6-TRISULFONIC ACID TRISODIUM SALT HYDRATE, 0.25%(W/V) 2,6- REMARK 280 NAPHTHALENEDISULFONIC ACID DISODIUM SALT, 0.25%(W/V) 4- REMARK 280 AMINOBENZOIC ACID, 0.25%(W/V) 5-SULFOSALICYLIC ACID DEHYDRATE., REMARK 280 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 33.40350 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: 990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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: 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 385 O HOH A 388 1.80 REMARK 500 O HOH A 494 O HOH A 495 2.10 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 ALA A 82 25.00 -140.54 REMARK 500 LYS A 116 -119.88 49.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 467 DISTANCE = 6.14 ANGSTROMS 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 95.3 REMARK 620 3 HEM A 201 NB 94.8 90.3 REMARK 620 4 HEM A 201 NC 87.5 177.1 88.9 REMARK 620 5 HEM A 201 ND 94.6 89.8 170.6 90.5 REMARK 620 6 HOH A 469 O 178.1 83.7 83.6 93.4 87.0 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 DBREF 4XMD 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 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *199(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 ALA A 46 O ALA A 57 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 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 2.03 LINK NE2 HIS A 60 FE BHEM A 201 1555 1555 2.48 LINK FE BHEM A 201 O HOH A 469 1555 1555 2.30 SITE 1 AC1 17 GLU A 27 TYR A 30 PHE A 41 PHE A 43 SITE 2 AC1 17 GLU A 56 LEU A 58 HIS A 60 PHE A 88 SITE 3 AC1 17 TYR A 107 VAL A 109 ILE A 121 ILE A 123 SITE 4 AC1 17 LEU A 135 HOH A 435 HOH A 454 HOH A 469 SITE 5 AC1 17 HOH A 477 CRYST1 38.312 66.807 39.026 90.00 116.87 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 0.026101 0.000000 0.013227 0.00000 SCALE2 0.000000 0.014968 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028726 0.00000