HEADER METAL BINDING PROTEIN 17-AUG-11 3TGB TITLE CRYSTAL STRUCTURE OF L130R MUTANT OF NITROPHORIN 4 FROM RHODNIUS TITLE 2 PROLIXUS COMPLEXED WITH IMIDAZOLE AT PH 7.4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROPHORIN-4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NP4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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, LIPOCALIN, NITROPHORIN, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.OGATA,C.HE,M.KNIPP REVDAT 1 30-MAY-12 3TGB 0 JRNL AUTH C.HE,M.R.FUCHS,H.OGATA,M.KNIPP JRNL TITL GUANIDINE-FERROHEME COORDINATION IN THE MUTANT PROTEIN JRNL TITL 2 NITROPHORIN 4(L130R). JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 51 4470 2012 JRNL REFN ISSN 1433-7851 JRNL PMID 22334402 JRNL DOI 10.1002/ANIE.201108691 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 32436 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1708 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 21.7226 - 3.0881 1.00 2775 146 0.1611 0.1870 REMARK 3 2 3.0881 - 2.4522 1.00 2738 145 0.1599 0.1981 REMARK 3 3 2.4522 - 2.1425 1.00 2688 141 0.1284 0.1863 REMARK 3 4 2.1425 - 1.9468 1.00 2704 142 0.1257 0.1534 REMARK 3 5 1.9468 - 1.8073 1.00 2716 143 0.1207 0.1964 REMARK 3 6 1.8073 - 1.7008 1.00 2685 142 0.1161 0.1574 REMARK 3 7 1.7008 - 1.6156 1.00 2706 142 0.1165 0.1665 REMARK 3 8 1.6156 - 1.5453 1.00 2691 142 0.1200 0.1830 REMARK 3 9 1.5453 - 1.4859 1.00 2680 141 0.1241 0.1765 REMARK 3 10 1.4859 - 1.4346 1.00 2683 141 0.1473 0.2192 REMARK 3 11 1.4346 - 1.3898 1.00 2688 141 0.1657 0.2089 REMARK 3 12 1.3898 - 1.3500 1.00 2682 142 0.1866 0.2418 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.45 REMARK 3 B_SOL : 60.56 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.320 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) : 2.92200 REMARK 3 B22 (A**2) : -1.52530 REMARK 3 B33 (A**2) : -1.39670 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -3.71730 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 : 0.007 1648 REMARK 3 ANGLE : 1.103 2261 REMARK 3 CHIRALITY : 0.079 238 REMARK 3 PLANARITY : 0.004 296 REMARK 3 DIHEDRAL : 13.136 587 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 3TGB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-11. REMARK 100 THE RCSB ID CODE IS RCSB067446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 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 : SI 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 : 34144 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 21.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM PHOSPHATE, PH 7.4, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 34.85950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.52900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.85950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.52900 REMARK 290 SMTRY3 4 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 326 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 303 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 258 LIES ON A SPECIAL POSITION. 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 PHE A 18 56.22 -94.46 REMARK 500 GLN A 65 -0.16 79.15 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 185 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 59 NE2 REMARK 620 2 HEM A 185 NA 89.4 REMARK 620 3 HEM A 185 NB 90.4 89.4 REMARK 620 4 HEM A 185 NC 89.5 178.7 90.0 REMARK 620 5 HEM A 185 ND 89.1 89.4 178.7 91.1 REMARK 620 6 IMD A 186 N3 178.4 89.1 89.3 92.0 91.3 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 185 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 186 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TGA RELATED DB: PDB REMARK 900 RELATED ID: 3TGC RELATED DB: PDB DBREF 3TGB A 1 184 UNP Q94734 NP4_RHOPR 22 205 SEQADV 3TGB ARG A 130 UNP Q94734 LEU 151 ENGINEERED MUTATION SEQRES 1 A 184 ALA CYS THR LYS ASN ALA ILE ALA GLN THR GLY PHE ASN SEQRES 2 A 184 LYS ASP LYS TYR PHE ASN GLY ASP VAL TRP TYR VAL THR SEQRES 3 A 184 ASP TYR LEU ASP LEU GLU PRO ASP ASP VAL PRO LYS ARG SEQRES 4 A 184 TYR CYS ALA ALA LEU ALA ALA GLY THR ALA SER GLY LYS SEQRES 5 A 184 LEU LYS GLU ALA LEU TYR HIS TYR ASP PRO LYS THR GLN SEQRES 6 A 184 ASP THR PHE TYR ASP VAL SER GLU LEU GLN VAL GLU SER SEQRES 7 A 184 LEU GLY LYS TYR THR ALA ASN PHE LYS LYS VAL ASP LYS SEQRES 8 A 184 ASN GLY ASN VAL LYS VAL ALA VAL THR ALA GLY ASN TYR SEQRES 9 A 184 TYR THR PHE THR VAL MET TYR ALA ASP ASP SER SER ALA SEQRES 10 A 184 LEU ILE HIS THR CYS LEU HIS LYS GLY ASN LYS ASP ARG SEQRES 11 A 184 GLY ASP LEU TYR ALA VAL LEU ASN ARG ASN LYS ASP ALA SEQRES 12 A 184 ALA ALA GLY ASP LYS VAL LYS SER ALA VAL SER ALA ALA SEQRES 13 A 184 THR LEU GLU PHE SER LYS PHE ILE SER THR LYS GLU ASN SEQRES 14 A 184 ASN CYS ALA TYR ASP ASN ASP SER LEU LYS SER LEU LEU SEQRES 15 A 184 THR LYS HET HEM A 185 43 HET IMD A 186 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 *189(H2 O) HELIX 1 1 ASN A 13 PHE A 18 1 6 HELIX 2 2 GLY A 146 ALA A 156 1 11 HELIX 3 3 GLU A 159 PHE A 163 5 5 HELIX 4 4 ASP A 174 LEU A 182 1 9 SHEET 1 A 7 VAL A 95 VAL A 97 0 SHEET 2 A 7 LYS A 81 VAL A 89 -1 N LYS A 88 O LYS A 96 SHEET 3 A 7 THR A 67 SER A 78 -1 N GLN A 75 O THR A 83 SHEET 4 A 7 LYS A 52 TYR A 60 -1 N LEU A 53 O LEU A 74 SHEET 5 A 7 CYS A 41 ALA A 49 -1 N GLY A 47 O LYS A 54 SHEET 6 A 7 VAL A 22 ASP A 30 -1 N TRP A 23 O LEU A 44 SHEET 7 A 7 ILE A 164 SER A 165 -1 O ILE A 164 N TYR A 28 SHEET 1 B 7 VAL A 95 VAL A 97 0 SHEET 2 B 7 LYS A 81 VAL A 89 -1 N LYS A 88 O LYS A 96 SHEET 3 B 7 ASN A 103 ALA A 112 -1 O TYR A 105 N ALA A 84 SHEET 4 B 7 SER A 116 LYS A 125 -1 O HIS A 124 N TYR A 104 SHEET 5 B 7 LEU A 133 ASN A 138 -1 O LEU A 137 N ALA A 117 SHEET 6 B 7 VAL A 22 ASP A 30 -1 N TYR A 24 O ASN A 138 SHEET 7 B 7 ILE A 164 SER A 165 -1 O ILE A 164 N TYR A 28 SSBOND 1 CYS A 2 CYS A 122 1555 1555 2.04 SSBOND 2 CYS A 41 CYS A 171 1555 1555 2.00 LINK NE2 HIS A 59 FE HEM A 185 1555 1555 2.05 LINK FE HEM A 185 N3 IMD A 186 1555 1555 2.06 SITE 1 AC1 19 TYR A 28 VAL A 36 PRO A 37 TYR A 40 SITE 2 AC1 19 GLU A 55 LEU A 57 HIS A 59 ASP A 70 SITE 3 AC1 19 PHE A 86 LYS A 88 TYR A 105 PHE A 107 SITE 4 AC1 19 LEU A 123 LYS A 125 ARG A 130 LEU A 133 SITE 5 AC1 19 IMD A 186 HOH A 290 HOH A 389 SITE 1 AC2 4 LEU A 123 LEU A 133 HEM A 185 HOH A 250 CRYST1 69.719 43.058 52.469 90.00 94.43 90.00 C 1 2 1 4 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 0.014343 0.000000 0.001110 0.00000 SCALE2 0.000000 0.023224 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019116 0.00000