HEADER OXIDOREDUCTASE 24-JUL-15 5CU9
TITLE CANDIDA ALBICANS SUPEROXIDE DISMUTASE 5 (SOD5), APO
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CELL SURFACE CU-ONLY SUPEROXIDE DISMUTASE 5;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 27-181;
COMPND 5 SYNONYM: PREDICTED GPI-ANCHORED PROTEIN 3;
COMPND 6 EC: 1.15.1.1;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDA ALBICANS (STRAIN SC5314 / ATCC MYA-
SOURCE 3 2876);
SOURCE 4 ORGANISM_COMMON: YEAST;
SOURCE 5 ORGANISM_TAXID: 237561;
SOURCE 6 STRAIN: SC5314 / ATCC MYA-2876;
SOURCE 7 GENE: SOD5, PGA3, SOD31, CAO19.2060, CAO19.9607;
SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PAG8H
KEYWDS ANTIOXIDANT, OXIDATIVE BURST, OXIDOREDUCTASE, ZINC LOOP, DISULFIDE
KEYWDS 2 BOND, EXTRACELLULAR
EXPDTA X-RAY DIFFRACTION
AUTHOR J.J.WANINGER-SARONI,A.B.TAYLOR,P.J.HART,A.GALALELDEEN
REVDAT 2 27-SEP-23 5CU9 1 REMARK
REVDAT 1 27-JUL-16 5CU9 0
JRNL AUTH J.J.WANINGER-SARONI,A.B.TAYLOR,P.J.HART,A.GALALELDEEN
JRNL TITL CANDIDA ALBICANS SUPEROXIDE DISMUTASE 5 (SOD5), APO
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.48 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1692
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) : 1.48
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.44
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 3 NUMBER OF REFLECTIONS : 22891
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.207
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.257
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.710
REMARK 3 FREE R VALUE TEST SET COUNT : 1994
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 51.4686 - 3.5666 0.94 1546 148 0.1690 0.1969
REMARK 3 2 3.5666 - 2.8310 0.96 1491 142 0.1889 0.2540
REMARK 3 3 2.8310 - 2.4732 0.98 1502 144 0.2055 0.2697
REMARK 3 4 2.4732 - 2.2470 0.99 1507 144 0.2049 0.2463
REMARK 3 5 2.2470 - 2.0860 0.99 1501 144 0.2024 0.2860
REMARK 3 6 2.0860 - 1.9630 0.99 1479 142 0.2029 0.2694
REMARK 3 7 1.9630 - 1.8647 0.99 1499 142 0.2058 0.2821
REMARK 3 8 1.8647 - 1.7835 1.00 1499 144 0.2176 0.2805
REMARK 3 9 1.7835 - 1.7148 0.99 1454 136 0.2503 0.2862
REMARK 3 10 1.7148 - 1.6557 1.00 1494 143 0.2702 0.3877
REMARK 3 11 1.6557 - 1.6039 1.00 1495 143 0.2872 0.3529
REMARK 3 12 1.6039 - 1.5580 1.00 1467 140 0.3041 0.3615
REMARK 3 13 1.5580 - 1.5170 1.00 1481 141 0.3207 0.3839
REMARK 3 14 1.5170 - 1.4800 1.00 1482 141 0.3529 0.4225
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) : 35.180
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 20.40
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.70
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 : 0.005 1189
REMARK 3 ANGLE : 0.938 1618
REMARK 3 CHIRALITY : 0.068 180
REMARK 3 PLANARITY : 0.004 213
REMARK 3 DIHEDRAL : 10.606 430
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 5CU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-15.
REMARK 100 THE DEPOSITION ID IS D_1000212191.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-FEB-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 24-ID-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22964
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480
REMARK 200 RESOLUTION RANGE LOW (A) : 102.870
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 200 DATA REDUNDANCY : 4.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.04200
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 5.10
REMARK 200 R MERGE FOR SHELL (I) : 0.63400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300
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: 4N3T
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 37.92
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M AMMONIUM SULFATE, 0.1 M HEPES,
REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING 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 17.26550
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.43750
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.84950
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.43750
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.26550
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.84950
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 VAL A 26
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 ASN A 53 31.46 -83.79
REMARK 500 GLU A 91 -143.74 60.72
REMARK 500 PHE A 94 99.41 -66.73
REMARK 500 ASN A 98 103.99 -55.82
REMARK 500 LEU A 148 -158.44 -95.49
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4N3T RELATED DB: PDB
REMARK 900 RELATED ID: 4N3U RELATED DB: PDB
DBREF 5CU9 A 27 181 UNP Q5AD07 SOD5_CANAL 27 181
SEQADV 5CU9 GLY A 23 UNP Q5AD07 EXPRESSION TAG
SEQADV 5CU9 ALA A 24 UNP Q5AD07 EXPRESSION TAG
SEQADV 5CU9 MET A 25 UNP Q5AD07 EXPRESSION TAG
SEQADV 5CU9 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 SO4 A 301 5
HET SO4 A 302 5
HETNAM SO4 SULFATE ION
FORMUL 2 SO4 2(O4 S 2-)
FORMUL 4 HOH *59(H2 O)
HELIX 1 AA1 PRO A 66 GLY A 70 5 5
HELIX 2 AA2 ASN A 86 GLU A 91 5 6
HELIX 3 AA3 THR A 105 HIS A 109 5 5
HELIX 4 AA4 ASP A 113 GLY A 119 1 7
SHEET 1 AA1 7 TYR A 74 HIS A 77 0
SHEET 2 AA1 7 SER A 149 HIS A 153 -1 O SER A 149 N HIS A 77
SHEET 3 AA1 7 ARG A 159 LEU A 167 -1 O LEU A 160 N ILE A 152
SHEET 4 AA1 7 LEU A 30 PHE A 34 -1 N ILE A 31 O THR A 166
SHEET 5 AA1 7 GLU A 43 PRO A 50 -1 O GLY A 44 N PHE A 34
SHEET 6 AA1 7 VAL A 56 LYS A 63 -1 O SER A 57 N THR A 49
SHEET 7 AA1 7 SER A 125 ASP A 132 -1 O TYR A 130 N VAL A 58
SSBOND 1 CYS A 87 CYS A 162 1555 1555 2.08
CISPEP 1 GLY A 70 PRO A 71 0 -1.86
SITE 1 AC1 9 ASN A 41 PRO A 66 SER A 84 ASN A 86
SITE 2 AC1 9 ALA A 89 HOH A 401 HOH A 402 HOH A 414
SITE 3 AC1 9 HOH A 441
SITE 1 AC2 3 THR A 37 SER A 38 ASN A 156
CRYST1 34.531 37.699 102.875 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 0.028959 0.000000 0.000000 0.00000
SCALE2 0.000000 0.026526 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009721 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
