PDB Short entry for 3KBF HEADER OXIDOREDUCTASE 20-OCT-09 3KBF TITLE C. ELEGANS CU,ZN SUPEROXIDE DISMUTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [CU-ZN]; COMPND 3 CHAIN: A; COMPND 4 EC: 1.15.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: C15F1.7, SOD-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PAED4 KEYWDS CU-ZN SUPEROXIDE DISMUTASE, ANTIOXIDANT, OXIDOREDUCTASE, NEMATODE, KEYWDS 2 DISULFIDE BOND, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR O.N.PAKHOMOVA,A.B.TAYLOR,J.P.SCHUERMANN,V.L.CULOTTA,P.J.HART REVDAT 1 03-NOV-10 3KBF 0 JRNL AUTH O.N.PAKHOMOVA,A.B.TAYLOR,J.P.SCHUERMANN,V.L.CULOTTA,P.J.HART JRNL TITL X-RAY CRYSTAL STRUCTURE OF C. ELEGANS CU,ZN SUPEROXIDE JRNL TITL 2 DISMUTASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 36365 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1828 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 32.9364 - 3.0547 1.00 2859 170 0.1645 0.1545 REMARK 3 2 3.0547 - 2.4249 1.00 2782 150 0.1623 0.1702 REMARK 3 3 2.4249 - 2.1184 1.00 2765 131 0.1369 0.1730 REMARK 3 4 2.1184 - 1.9247 1.00 2728 148 0.1208 0.1318 REMARK 3 5 1.9247 - 1.7868 1.00 2690 152 0.1091 0.1271 REMARK 3 6 1.7868 - 1.6815 1.00 2720 162 0.1113 0.1271 REMARK 3 7 1.6815 - 1.5972 1.00 2689 151 0.1149 0.1401 REMARK 3 8 1.5972 - 1.5277 1.00 2688 132 0.1089 0.1385 REMARK 3 9 1.5277 - 1.4689 1.00 2712 131 0.1138 0.1567 REMARK 3 10 1.4689 - 1.4182 0.99 2691 130 0.1182 0.1654 REMARK 3 11 1.4182 - 1.3739 0.98 2641 151 0.1278 0.1802 REMARK 3 12 1.3739 - 1.3346 0.93 2521 112 0.1537 0.1715 REMARK 3 13 1.3346 - 1.3000 0.76 2051 108 0.1779 0.2208 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 : 0.36 REMARK 3 B_SOL : 39.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.30260 REMARK 3 B22 (A**2) : -3.15060 REMARK 3 B33 (A**2) : 0.84800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 1171 REMARK 3 ANGLE : 1.014 1592 REMARK 3 CHIRALITY : 0.066 182 REMARK 3 PLANARITY : 0.004 211 REMARK 3 DIHEDRAL : 15.047 419 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 3KBF COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-OCT-09. REMARK 100 THE RCSB ID CODE IS RCSB055781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36429 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 11.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 65% MPD, PH 6.9, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 55.24400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.24400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 19.60200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.49300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.60200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.49300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.24400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.60200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 34.49300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.24400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.60200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 34.49300 REMARK 290 SMTRY3 8 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: 2060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -55.24400 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 157 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 CU A 158 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 45 ND1 REMARK 620 2 HIS A 47 NE2 135.2 REMARK 620 3 HIS A 119 NE2 100.5 121.4 REMARK 620 4 SO4 A 160 O3 96.6 83.2 71.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 159 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 62 ND1 REMARK 620 2 HIS A 70 ND1 102.1 REMARK 620 3 HIS A 79 ND1 111.9 122.8 REMARK 620 4 ASP A 82 OD1 105.4 98.1 114.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 159 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 160 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KBE RELATED DB: PDB DBREF 3KBF A 1 157 UNP P34697 SODC_CAEEL 24 180 SEQRES 1 A 157 SER ASN ARG ALA VAL ALA VAL LEU ARG GLY GLU THR VAL SEQRES 2 A 157 THR GLY THR ILE TRP ILE THR GLN LYS SER GLU ASN ASP SEQRES 3 A 157 GLN ALA VAL ILE GLU GLY GLU ILE LYS GLY LEU THR PRO SEQRES 4 A 157 GLY LEU HIS GLY PHE HIS VAL HIS GLN TYR GLY ASP SER SEQRES 5 A 157 THR ASN GLY CYS ILE SER ALA GLY PRO HIS PHE ASN PRO SEQRES 6 A 157 PHE GLY LYS THR HIS GLY GLY PRO LYS SER GLU ILE ARG SEQRES 7 A 157 HIS VAL GLY ASP LEU GLY ASN VAL GLU ALA GLY ALA ASP SEQRES 8 A 157 GLY VAL ALA LYS ILE LYS LEU THR ASP THR LEU VAL THR SEQRES 9 A 157 LEU TYR GLY PRO ASN THR VAL VAL GLY ARG SER MET VAL SEQRES 10 A 157 VAL HIS ALA GLY GLN ASP ASP LEU GLY GLU GLY VAL GLY SEQRES 11 A 157 ASP LYS ALA GLU GLU SER LYS LYS THR GLY ASN ALA GLY SEQRES 12 A 157 ALA ARG ALA ALA CYS GLY VAL ILE ALA LEU ALA ALA PRO SEQRES 13 A 157 GLN HET CU A 158 2 HET ZN A 159 1 HET SO4 A 160 5 HETNAM CU COPPER (II) ION HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 CU CU 2+ FORMUL 3 ZN ZN 2+ FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *221(H2 O) HELIX 1 1 CYS A 56 GLY A 60 5 5 HELIX 2 2 VAL A 129 ASP A 131 5 3 HELIX 3 3 LYS A 132 GLY A 140 1 9 SHEET 1 A 9 ASN A 2 LEU A 8 0 SHEET 2 A 9 THR A 14 GLN A 21 -1 O ILE A 19 N ALA A 4 SHEET 3 A 9 ALA A 28 LYS A 35 -1 O GLU A 31 N TRP A 18 SHEET 4 A 9 ALA A 94 ASP A 100 -1 O LEU A 98 N ILE A 30 SHEET 5 A 9 ASP A 82 ALA A 88 -1 N GLU A 87 O LYS A 95 SHEET 6 A 9 GLY A 40 HIS A 47 -1 N GLY A 40 O ALA A 88 SHEET 7 A 9 SER A 115 HIS A 119 -1 O HIS A 119 N GLY A 43 SHEET 8 A 9 ARG A 145 ALA A 154 -1 O GLY A 149 N MET A 116 SHEET 9 A 9 ASN A 2 LEU A 8 -1 N VAL A 5 O ALA A 152 SSBOND 1 CYS A 56 CYS A 148 1555 1555 2.10 LINK ND1 HIS A 45 CU A CU A 158 1555 1555 2.07 LINK NE2 HIS A 47 CU A CU A 158 1555 1555 2.04 LINK NE2 HIS A 47 CU B CU A 158 1555 1555 2.17 LINK ND1 HIS A 62 ZN ZN A 159 1555 1555 2.06 LINK ND1 HIS A 70 ZN ZN A 159 1555 1555 2.09 LINK ND1 HIS A 79 ZN ZN A 159 1555 1555 2.05 LINK OD1 ASP A 82 ZN ZN A 159 1555 1555 1.98 LINK NE2 HIS A 119 CU A CU A 158 1555 1555 2.11 LINK NE2 HIS A 119 CU B CU A 158 1555 1555 2.02 LINK CU B CU A 158 O3 SO4 A 160 1555 1555 2.19 LINK ND1 HIS A 45 CU B CU A 158 1555 1555 2.44 SITE 1 AC1 6 HIS A 45 HIS A 47 HIS A 62 HIS A 119 SITE 2 AC1 6 SO4 A 160 HOH A 304 SITE 1 AC2 4 HIS A 62 HIS A 70 HIS A 79 ASP A 82 SITE 1 AC3 10 HIS A 47 HIS A 62 HIS A 119 THR A 139 SITE 2 AC3 10 ARG A 145 CU A 158 HOH A 304 HOH A 324 SITE 3 AC3 10 HOH A 325 HOH A 356 CRYST1 39.204 68.986 110.488 90.00 90.00 90.00 C 2 2 21 8 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 0.025508 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014496 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009051 0.00000