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- PDB-1cbj: CRYSTAL STRUCTURE OF BOVINE SUPEROXIDE DISMUTASE CRYSTAL. -

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Basic information

Entry
Database: PDB / ID: 1cbj
TitleCRYSTAL STRUCTURE OF BOVINE SUPEROXIDE DISMUTASE CRYSTAL.
ComponentsPROTEIN (SUPEROXIDE DISMUTASE)
KeywordsOXIDOREDUCTASE / CUZN SUPEROXIDE DISMUTASE / FUNCTIONAL ASYMMETRY / DISORDER
Function / homology
Function and homology information


Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization ...Platelet degranulation / Detoxification of Reactive Oxygen Species / positive regulation of catalytic activity / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / superoxide dismutase activity / transmission of nerve impulse / regulation of multicellular organism growth / response to axon injury / ovarian follicle development / glutathione metabolic process / embryo implantation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of cytokine production / regulation of mitochondrial membrane potential / locomotory behavior / response to hydrogen peroxide / sensory perception of sound / regulation of blood pressure / protein polyubiquitination / ubiquitin-protein transferase activity / peroxisome / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / positive regulation of MAPK cascade / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleus / cytoplasm / 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 / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHough, M.A. / Hasnain, S.S.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystallographic structures of bovine copper-zinc superoxide dismutase reveal asymmetry in two subunits: functionally important three and five coordinate copper sites captured in the same crystal.
Authors: Hough, M.A. / Hasnain, S.S.
History
DepositionFeb 26, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 3, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (SUPEROXIDE DISMUTASE)
B: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4056
Polymers31,1472
Non-polymers2584
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.770, 51.130, 147.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein PROTEIN (SUPEROXIDE DISMUTASE)


Mass: 15573.337 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ONE COPPER(II) SITE, ONE CU(I) SITE. / Source: (natural) Bos taurus (domestic cattle) / Cell: ERYTHROCYTES / References: UniProt: P00442, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsREDUCED COPPER OXIDIZED COPPER ZINC SITE ZINC SITE SUBUNIT A CONTAINS A THREE COORDINATE, CU(I) ...REDUCED COPPER OXIDIZED COPPER ZINC SITE ZINC SITE SUBUNIT A CONTAINS A THREE COORDINATE, CU(I) SITE. SUBUNIT B CONTAINS A FIVE COORDINATE, CU(II) SITE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 55 %
Crystal growpH: 6.5 / Details: pH 6.50
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NACL11
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1PEG40001reservoir
2sodium chloride1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 4, 1997 / Details: MIRRORS
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.65→15 Å / Num. obs: 39196 / % possible obs: 89.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.3
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.6 / % possible all: 68.2
Reflection
*PLUS
% possible obs: 89.1 % / Num. measured all: 172498
Reflection shell
*PLUS
% possible obs: 68.2 % / Redundancy: 4.3 % / Mean I/σ(I) obs: 4.6

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Processing

Software
NameClassification
DENZOdata reduction
CCP4data reduction
AMoREphasing
REFMACrefinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COB

1cob


Resolution: 1.65→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: XPLOR SIMULATED ANNEALING ALSO USED
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1195 3 %RANDOM
Rwork0.185 ---
obs0.186 44556 90 %-
all-44556 --
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 4 232 2402
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4222
X-RAY DIFFRACTIONp_mcangle_it2.1433
X-RAY DIFFRACTIONp_scbond_it2.2692
X-RAY DIFFRACTIONp_scangle_it3.5453
X-RAY DIFFRACTIONp_plane_restr0.022
X-RAY DIFFRACTIONp_chiral_restr0.01
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.2550.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1080.3
X-RAY DIFFRACTIONp_planar_tor3.87
X-RAY DIFFRACTIONp_staggered_tor13.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor37.420
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.2

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