HEADER OXIDOREDUCTASE 07-OCT-13 4N3T TITLE CANDIDA ALBICANS SUPEROXIDE DISMUTASE 5 (SOD5), CU(I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: POTENTIAL SECRETED CU/ZN SUPEROXIDE DISMUTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 27-181; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDA ALBICANS; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 237561; SOURCE 5 STRAIN: SC5314 / ATCC MYA-2876; SOURCE 6 GENE: CAO19.2060, CAO19.9607, SOD31, SOD5; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PAG8H KEYWDS ANTIOXIDANT, OXIDATIVE BURST, OXIDOREDUCTASE, ZINC LOOP, DISULFIDE KEYWDS 2 BOND, EXTRACELLULAR EXPDTA X-RAY DIFFRACTION AUTHOR A.GALALELDEEN,A.B.TAYLOR,J.J.WANINGER-SARONI,S.P.HOLLOWAY,P.J.HART REVDAT 3 20-SEP-23 4N3T 1 REMARK SEQADV LINK REVDAT 2 14-MAY-14 4N3T 1 JRNL REVDAT 1 09-APR-14 4N3T 0 JRNL AUTH J.E.GLEASON,A.GALALELDEEN,R.L.PETERSON,A.B.TAYLOR, JRNL AUTH 2 S.P.HOLLOWAY,J.WANINGER-SARONI,B.P.CORMACK,D.E.CABELLI, JRNL AUTH 3 P.J.HART,V.C.CULOTTA JRNL TITL CANDIDA ALBICANS SOD5 REPRESENTS THE PROTOTYPE OF AN JRNL TITL 2 UNPRECEDENTED CLASS OF CU-ONLY SUPEROXIDE DISMUTASES JRNL TITL 3 REQUIRED FOR PATHOGEN DEFENSE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 5866 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24711423 JRNL DOI 10.1073/PNAS.1400137111 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.3_1479) 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 28837 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 31.7278 - 3.3731 0.99 2054 154 0.1519 0.1636 REMARK 3 2 3.3731 - 2.6778 0.99 1956 144 0.1466 0.1950 REMARK 3 3 2.6778 - 2.3394 1.00 1950 146 0.1437 0.1969 REMARK 3 4 2.3394 - 2.1256 0.99 1913 143 0.1367 0.1956 REMARK 3 5 2.1256 - 1.9732 0.99 1927 144 0.1280 0.1621 REMARK 3 6 1.9732 - 1.8569 0.99 1903 140 0.1270 0.1613 REMARK 3 7 1.8569 - 1.7639 1.00 1901 142 0.1258 0.2099 REMARK 3 8 1.7639 - 1.6871 1.00 1902 141 0.1337 0.1629 REMARK 3 9 1.6871 - 1.6222 1.00 1876 140 0.1393 0.1856 REMARK 3 10 1.6222 - 1.5662 1.00 1895 141 0.1531 0.2656 REMARK 3 11 1.5662 - 1.5172 1.00 1899 142 0.1658 0.2268 REMARK 3 12 1.5172 - 1.4739 1.00 1902 141 0.1923 0.2525 REMARK 3 13 1.4739 - 1.4351 1.00 1871 141 0.2023 0.2274 REMARK 3 14 1.4351 - 1.4000 1.00 1889 140 0.2325 0.2896 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.60 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 1204 REMARK 3 ANGLE : 1.092 1644 REMARK 3 CHIRALITY : 0.072 184 REMARK 3 PLANARITY : 0.004 215 REMARK 3 DIHEDRAL : 9.986 439 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 4N3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-12 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 102.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04300 REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.56900 REMARK 200 FOR SHELL : 2.500 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 1AZV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M AMMONIUM SULFATE, 0.1 M BICINE, REMARK 280 PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.23800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.08350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.23300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.08350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.23800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.23300 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 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 GLY A 23 REMARK 465 ALA A 24 REMARK 465 MET A 25 REMARK 465 MET A 179 REMARK 465 SER A 180 REMARK 465 ASN A 181 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 GLU A 91 -137.82 59.75 REMARK 500 ASN A 98 74.11 55.21 REMARK 500 LEU A 148 -159.69 -94.31 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 CU1 A 201 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 75 ND1 REMARK 620 2 HIS A 77 NE2 133.6 REMARK 620 3 HIS A 153 NE2 106.9 119.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU1 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4N3U RELATED DB: PDB DBREF 4N3T A 27 181 UNP Q5AD07 Q5AD07_CANAL 27 181 SEQADV 4N3T GLY A 23 UNP Q5AD07 EXPRESSION TAG SEQADV 4N3T ALA A 24 UNP Q5AD07 EXPRESSION TAG SEQADV 4N3T MET A 25 UNP Q5AD07 EXPRESSION TAG SEQADV 4N3T VAL A 26 UNP Q5AD07 EXPRESSION TAG SEQRES 1 A 159 GLY ALA MET VAL SER PRO SER LEU ILE ALA LYS PHE GLU SEQRES 2 A 159 LYS THR SER LYS SER ASN ILE GLU GLY THR ILE LYS PHE SEQRES 3 A 159 THR PRO ALA ASN ASN GLY THR VAL SER VAL SER VAL ASP SEQRES 4 A 159 LEU LYS GLY LEU PRO SER ASP ILE GLY PRO PHE PRO TYR SEQRES 5 A 159 HIS VAL HIS GLU LYS PRO VAL PRO ALA SER LYS ASN CYS SEQRES 6 A 159 SER ALA THR GLU ASN HIS PHE ASN PRO TYR ASN GLY THR SEQRES 7 A 159 VAL ARG ALA ALA THR PRO ALA ALA HIS GLU VAL GLY ASP SEQRES 8 A 159 LEU ALA GLY LYS HIS GLY ASN ILE MET GLY GLU SER TYR SEQRES 9 A 159 LYS THR GLU TYR ASP ASP SER TYR ILE SER LEU ASN GLU SEQRES 10 A 159 LYS SER ARG SER TYR ILE GLY GLY LEU SER ILE VAL ILE SEQRES 11 A 159 HIS ALA ASN ASN GLY THR ARG LEU ASN CYS ALA ASN ILE SEQRES 12 A 159 THR LEU LEU ASP GLU GLY HIS GLY ASN ALA ASN THR THR SEQRES 13 A 159 MET SER ASN HET CU1 A 201 1 HET SO4 A 202 5 HET SO4 A 203 5 HET TRS A 204 8 HETNAM CU1 COPPER (I) ION HETNAM SO4 SULFATE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 CU1 CU 1+ FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *145(H2 O) HELIX 1 1 PRO A 66 GLY A 70 5 5 HELIX 2 2 ASN A 86 GLU A 91 5 6 HELIX 3 3 THR A 105 HIS A 109 5 5 HELIX 4 4 ASP A 113 GLY A 119 1 7 SHEET 1 A 7 TYR A 74 HIS A 77 0 SHEET 2 A 7 SER A 149 HIS A 153 -1 O SER A 149 N HIS A 77 SHEET 3 A 7 ARG A 159 LEU A 167 -1 O ASN A 161 N ILE A 152 SHEET 4 A 7 LEU A 30 PHE A 34 -1 N ILE A 31 O THR A 166 SHEET 5 A 7 GLU A 43 ALA A 51 -1 O PHE A 48 N LEU A 30 SHEET 6 A 7 THR A 55 LYS A 63 -1 O SER A 57 N THR A 49 SHEET 7 A 7 TYR A 126 ASP A 132 -1 O TYR A 130 N VAL A 58 SSBOND 1 CYS A 87 CYS A 162 1555 1555 2.46 LINK ND1 HIS A 75 CU CU1 A 201 1555 1555 2.06 LINK NE2 HIS A 77 CU CU1 A 201 1555 1555 1.96 LINK NE2 HIS A 153 CU CU1 A 201 1555 1555 2.00 CISPEP 1 GLY A 70 PRO A 71 0 0.20 SITE 1 AC1 4 HIS A 75 HIS A 77 HIS A 93 HIS A 153 SITE 1 AC2 4 THR A 37 SER A 38 ASN A 156 HOH A 410 SITE 1 AC3 9 ASN A 41 PRO A 66 SER A 84 ASN A 86 SITE 2 AC3 9 HOH A 326 HOH A 397 HOH A 398 HOH A 440 SITE 3 AC3 9 HOH A 443 SITE 1 AC4 7 HIS A 75 HIS A 93 HIS A 153 GLY A 157 SITE 2 AC4 7 ARG A 159 HOH A 330 HOH A 441 CRYST1 34.476 40.466 102.167 90.00 90.00 90.00 P 21 21 21 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 0.029006 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024712 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009788 0.00000