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- PDB-1yso: YEAST CU, ZN SUPEROXIDE DISMUTASE WITH THE REDUCED BRIDGE BROKEN -

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Basic information

Entry
Database: PDB / ID: 1yso
TitleYEAST CU, ZN SUPEROXIDE DISMUTASE WITH THE REDUCED BRIDGE BROKEN
ComponentsYEAST CU, ZN SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE (SUPEROXIDE ACCEPTOR) / COPPER / ZINC
Function / homology
Function and homology information


superoxide dismutase complex / protein maturation by copper ion transfer / negative regulation of cellular respiration / fungal-type cell wall organization / Platelet degranulation / Detoxification of Reactive Oxygen Species / intracellular zinc ion homeostasis / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity ...superoxide dismutase complex / protein maturation by copper ion transfer / negative regulation of cellular respiration / fungal-type cell wall organization / Platelet degranulation / Detoxification of Reactive Oxygen Species / intracellular zinc ion homeostasis / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / intracellular copper ion homeostasis / removal of superoxide radicals / mitochondrial intermembrane space / peroxisome / protein stabilization / copper ion binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytosol
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.73 Å
AuthorsParge, H.E. / Crane, B.R. / Tsang, J. / Tainer, J.A.
CitationJournal: Biochemistry / Year: 1996
Title: Unusual trigonal-planar copper configuration revealed in the atomic structure of yeast copper-zinc superoxide dismutase.
Authors: Ogihara, N.L. / Parge, H.E. / Hart, P.J. / Weiss, M.S. / Goto, J.J. / Crane, B.R. / Tsang, J. / Slater, K. / Roe, J.A. / Valentine, J.S. / Eisenberg, D. / Tainer, J.A.
History
DepositionDec 21, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.pdbx_collection_date / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YEAST CU, ZN SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8723
Polymers15,7431
Non-polymers1292
Water2,252125
1
A: YEAST CU, ZN SUPEROXIDE DISMUTASE
hetero molecules

A: YEAST CU, ZN SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7456
Polymers31,4872
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z1
Unit cell
Length a, b, c (Å)119.330, 119.330, 75.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-278-

HOH

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Components

#1: Protein YEAST CU, ZN SUPEROXIDE DISMUTASE / YEAST CU / ZN SOD


Mass: 15743.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: REDUCED CUI BRIDGE BROKEN / Source: (natural) Candida albicans (yeast) / References: UniProt: P00445, superoxide dismutase
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 61.7 %
Crystal grow
*PLUS
pH: 7.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMphosphate1drop
22.0-2.3 Mammonium sulfate1reservoir
350 mMTris-HCl1reservoir
450 mM1reservoirNaCl
50.001 %(w/v)1reservoirNaN3

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→44 Å / Num. obs: 20002 / % possible obs: 92.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Num. measured all: 102086
Reflection shell
*PLUS
Highest resolution: 1.73 Å / Lowest resolution: 1.8 Å / % possible obs: 40.9 %

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Processing

Software
NameClassification
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 1.73→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.182 -
obs0.182 17682
Refinement stepCycle: LAST / Resolution: 1.73→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 2 125 1233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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