HEADER OXIDOREDUCTASE 07-OCT-13 4N3U TITLE CANDIDA ALBICANS SUPEROXIDE DISMUTASE 5 (SOD5), CU(II) 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 4N3U 1 REMARK SEQADV LINK REVDAT 2 14-MAY-14 4N3U 1 JRNL REVDAT 1 09-APR-14 4N3U 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. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 14787 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1479 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 26.1031 - 3.8881 0.98 1308 146 0.1630 0.1893 REMARK 3 2 3.8881 - 3.0877 1.00 1220 135 0.1597 0.2072 REMARK 3 3 3.0877 - 2.6978 1.00 1233 137 0.1946 0.2081 REMARK 3 4 2.6978 - 2.4514 1.00 1212 134 0.1912 0.2348 REMARK 3 5 2.4514 - 2.2758 1.00 1202 134 0.1901 0.2068 REMARK 3 6 2.2758 - 2.1417 1.00 1203 134 0.1892 0.2552 REMARK 3 7 2.1417 - 2.0344 1.00 1181 132 0.1980 0.2289 REMARK 3 8 2.0344 - 1.9459 1.00 1194 132 0.1947 0.2795 REMARK 3 9 1.9459 - 1.8710 1.00 1196 132 0.2089 0.2705 REMARK 3 10 1.8710 - 1.8065 1.00 1178 132 0.2397 0.2892 REMARK 3 11 1.8065 - 1.7500 0.99 1181 131 0.2881 0.3372 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.80 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 : 0.007 1225 REMARK 3 ANGLE : 1.042 1674 REMARK 3 CHIRALITY : 0.042 187 REMARK 3 PLANARITY : 0.005 224 REMARK 3 DIHEDRAL : 10.783 450 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 4N3U 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_1000082717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14845 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.51300 REMARK 200 FOR SHELL : 3.200 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 (%): 40.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M SODIUM CITRATE, 0.1 M HEPES, PH REMARK 280 7.5, 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 17.23650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.99600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.97650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.99600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.23650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.97650 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 SER A 67 -55.76 -15.56 REMARK 500 GLU A 91 -137.45 57.70 REMARK 500 ASN A 95 58.89 -146.09 REMARK 500 LEU A 148 -158.86 -95.15 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 CU A 201 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 75 ND1 REMARK 620 2 HIS A 77 NE2 138.5 REMARK 620 3 HIS A 153 NE2 100.1 118.0 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 CU A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4N3T RELATED DB: PDB DBREF 4N3U A 27 181 UNP Q5AD07 Q5AD07_CANAL 27 181 SEQADV 4N3U GLY A 23 UNP Q5AD07 EXPRESSION TAG SEQADV 4N3U ALA A 24 UNP Q5AD07 EXPRESSION TAG SEQADV 4N3U MET A 25 UNP Q5AD07 EXPRESSION TAG SEQADV 4N3U 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 CU A 201 1 HET FLC A 202 13 HETNAM CU COPPER (II) ION HETNAM FLC CITRATE ANION FORMUL 2 CU CU 2+ FORMUL 3 FLC C6 H5 O7 3- FORMUL 4 HOH *132(H2 O) HELIX 1 1 ASN A 52 GLY A 54 5 3 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 LEU A 160 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 PRO A 50 -1 O GLY A 44 N PHE A 34 SHEET 6 A 7 VAL A 56 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 2.05 LINK ND1 HIS A 75 CU CU A 201 1555 1555 2.06 LINK NE2 HIS A 77 CU CU A 201 1555 1555 2.07 LINK NE2 HIS A 153 CU CU A 201 1555 1555 1.96 CISPEP 1 GLY A 70 PRO A 71 0 -2.59 SITE 1 AC1 5 HIS A 75 HIS A 77 HIS A 93 HIS A 153 SITE 2 AC1 5 FLC A 202 SITE 1 AC2 9 HIS A 75 HIS A 77 HIS A 93 HIS A 153 SITE 2 AC2 9 GLY A 157 ARG A 159 CU A 201 HOH A 330 SITE 3 AC2 9 HOH A 376 CRYST1 34.473 39.953 101.992 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 0.029008 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009805 0.00000