HEADER OXIDOREDUCTASE 20-OCT-09 3KBE TITLE METAL-FREE 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 2 06-SEP-23 3KBE 1 REMARK REVDAT 1 20-OCT-10 3KBE 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. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 55889 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2804 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 24.4456 - 2.9805 0.95 2968 156 0.1853 0.1997 REMARK 3 2 2.9805 - 2.3663 0.99 2987 159 0.1670 0.1589 REMARK 3 3 2.3663 - 2.0674 0.99 2973 156 0.1446 0.1575 REMARK 3 4 2.0674 - 1.8784 0.99 2920 154 0.1364 0.1499 REMARK 3 5 1.8784 - 1.7438 0.98 2885 150 0.1402 0.1858 REMARK 3 6 1.7438 - 1.6410 0.98 2883 153 0.1336 0.1732 REMARK 3 7 1.6410 - 1.5589 0.97 2844 147 0.1247 0.1482 REMARK 3 8 1.5589 - 1.4910 0.96 2827 146 0.1176 0.1551 REMARK 3 9 1.4910 - 1.4336 0.96 2805 147 0.1188 0.1330 REMARK 3 10 1.4336 - 1.3842 0.94 2759 148 0.1227 0.1383 REMARK 3 11 1.3842 - 1.3409 0.93 2737 139 0.1222 0.1533 REMARK 3 12 1.3409 - 1.3026 0.91 2669 144 0.1258 0.1463 REMARK 3 13 1.3026 - 1.2683 0.89 2568 137 0.1363 0.1613 REMARK 3 14 1.2683 - 1.2373 0.85 2497 132 0.1387 0.1719 REMARK 3 15 1.2373 - 1.2092 0.84 2436 130 0.1371 0.1463 REMARK 3 16 1.2092 - 1.1835 0.81 2350 121 0.1441 0.1685 REMARK 3 17 1.1835 - 1.1598 0.79 2330 117 0.1525 0.1860 REMARK 3 18 1.1598 - 1.1379 0.79 2265 128 0.1567 0.1384 REMARK 3 19 1.1379 - 1.1176 0.78 2248 117 0.1668 0.2377 REMARK 3 20 1.1176 - 1.1000 0.73 2134 123 0.1909 0.2304 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 : 0.45 REMARK 3 B_SOL : 75.85 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.630 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47510 REMARK 3 B22 (A**2) : -0.23110 REMARK 3 B33 (A**2) : -0.24400 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 1224 REMARK 3 ANGLE : 1.097 1683 REMARK 3 CHIRALITY : 0.069 191 REMARK 3 PLANARITY : 0.006 230 REMARK 3 DIHEDRAL : 15.262 448 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 3KBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 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 : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59043 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 29.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30000 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2C9V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BICINE, 2.4 M AMMONIUM SULFATE, REMARK 280 PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 40.62300 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 40.62300 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 20.10500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.16500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.10500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.16500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.62300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.10500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.16500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.62300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.10500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.16500 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: 1490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 -40.21000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.62300 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 253 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 336 LIES ON A SPECIAL POSITION. 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 122 REMARK 465 ASP A 123 REMARK 465 ASP A 124 REMARK 465 LEU A 125 REMARK 465 GLY A 126 REMARK 465 GLU A 127 REMARK 465 GLY A 128 REMARK 465 VAL A 129 REMARK 465 GLY A 130 REMARK 465 ASP A 131 REMARK 465 LYS A 132 REMARK 465 ALA A 133 REMARK 465 GLU A 134 REMARK 465 GLU A 135 REMARK 465 SER A 136 REMARK 465 LYS A 137 REMARK 465 LYS A 138 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KBF RELATED DB: PDB DBREF 3KBE 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 FORMUL 2 HOH *222(H2 O) HELIX 1 1 CYS A 56 GLY A 60 5 5 HELIX 2 2 GLY A 72 ILE A 77 5 6 SHEET 1 A 8 ASP A 82 VAL A 86 0 SHEET 2 A 8 HIS A 42 HIS A 47 -1 N HIS A 42 O VAL A 86 SHEET 3 A 8 SER A 115 HIS A 119 -1 O HIS A 119 N GLY A 43 SHEET 4 A 8 ARG A 145 LEU A 153 -1 O ALA A 146 N VAL A 118 SHEET 5 A 8 ARG A 3 LEU A 8 -1 N VAL A 5 O ALA A 152 SHEET 6 A 8 THR A 14 THR A 20 -1 O ILE A 19 N ALA A 4 SHEET 7 A 8 VAL A 29 LYS A 35 -1 O GLU A 31 N TRP A 18 SHEET 8 A 8 VAL A 93 LEU A 98 -1 O ILE A 96 N GLY A 32 SSBOND 1 CYS A 56 CYS A 148 1555 1555 2.12 CRYST1 40.210 92.330 81.246 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 0.024869 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010831 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012308 0.00000