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- PDB-1f1g: Crystal structure of yeast cuznsod exposed to nitric oxide -

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Basic information

Entry
Database: PDB / ID: 1f1g
TitleCrystal structure of yeast cuznsod exposed to nitric oxide
ComponentsCOPPER-ZINC SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / Nitric Oxide / CuZnSOD
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor / superoxide dismutase complex / negative regulation of cellular respiration / fungal-type cell wall organization / Platelet degranulation / Detoxification of Reactive Oxygen Species / copper ion transport / intracellular zinc ion homeostasis / cellular detoxification / superoxide metabolic process ...oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor / superoxide dismutase complex / negative regulation of cellular respiration / fungal-type cell wall organization / Platelet degranulation / Detoxification of Reactive Oxygen Species / copper ion transport / intracellular zinc ion homeostasis / cellular detoxification / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / intracellular copper ion homeostasis / removal of superoxide radicals / mitochondrial intermembrane space / cellular response to oxidative stress / 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 (Cu/Zn) / superoxide dismutase copper chaperone / 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-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / PHOSPHATE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.35 Å
AuthorsHart, P.J. / Ogihara, N.L. / Liu, H. / Nersissian, A.M. / Valentine, J.S. / Eisenberg, D.
CitationJournal: Biochemistry / Year: 1999
Title: A structure-based mechanism for copper-zinc superoxide dismutase.
Authors: Hart, P.J. / Balbirnie, M.M. / Ogihara, N.L. / Nersissian, A.M. / Weiss, M.S. / Valentine, J.S. / Eisenberg, D.
History
DepositionMay 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2014Group: Database references
Revision 1.4Feb 12, 2014Group: Derived calculations
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software
Revision 1.6Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COPPER-ZINC SUPEROXIDE DISMUTASE
B: COPPER-ZINC SUPEROXIDE DISMUTASE
C: COPPER-ZINC SUPEROXIDE DISMUTASE
D: COPPER-ZINC SUPEROXIDE DISMUTASE
E: COPPER-ZINC SUPEROXIDE DISMUTASE
F: COPPER-ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,59124
Polymers95,2486
Non-polymers1,34418
Water21,6181200
1
A: COPPER-ZINC SUPEROXIDE DISMUTASE
B: COPPER-ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1978
Polymers31,7492
Non-polymers4486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-16 kcal/mol
Surface area13640 Å2
MethodPISA
2
C: COPPER-ZINC SUPEROXIDE DISMUTASE
D: COPPER-ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1978
Polymers31,7492
Non-polymers4486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-16 kcal/mol
Surface area13530 Å2
MethodPISA
3
E: COPPER-ZINC SUPEROXIDE DISMUTASE
F: COPPER-ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1978
Polymers31,7492
Non-polymers4486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-16 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.500, 72.480, 72.470
Angle α, β, γ (deg.)109.20, 109.55, 109.21
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
COPPER-ZINC SUPEROXIDE DISMUTASE / CUZNSOD


Mass: 15874.587 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cellular location: CYTOPLASM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00445, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1200 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: ammonium sulfate, Tris-Hcl, NaCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. all: 1530112 / Num. obs: 233021 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.3
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.223 / Num. unique all: 22837 / % possible all: 92.5

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementResolution: 1.35→40 Å / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rwork0.171 -
all0.171 233021
obs-233021
Refinement stepCycle: LAST / Resolution: 1.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 42 1200 7878
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d2.1

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