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- PDB-1cb4: CRYSTAL STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE -

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Basic information

Entry
Database: PDB / ID: 1cb4
TitleCRYSTAL STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE
ComponentsPROTEIN (SUPEROXIDE DISMUTASE)
KeywordsOXIDOREDUCTASE / CUZN SUPEROXIDE DISMUTASE / TEMPERATURE FACTOR ASYMMETRY
Function / homology
Function and homology information


neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity ...neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / glutathione metabolic process / ovarian follicle development / embryo implantation / reactive oxygen species metabolic process / dendrite cytoplasm / removal of superoxide radicals / locomotory behavior / regulation of mitochondrial membrane potential / response to organic substance / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / regulation of blood pressure / peroxisome / protein polyubiquitination / ubiquitin-protein transferase activity / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / 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 / cytosol / cytoplasm
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 / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: PDBE / 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 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,3756
Polymers31,1192
Non-polymers2564
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.100, 199.180, 51.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein PROTEIN (SUPEROXIDE DISMUTASE)


Mass: 15559.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BOVINE ERYTHROCYTES / Source: (natural) Bos taurus (cattle) / References: UniProt: P00442, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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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: 4.31 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 277 K / pH: 6 / Details: pH 6.00, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NACLSodium chloride11
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
pH: 6.5 / 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: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 1997 / Details: MIRRORS
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 24270 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 16.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 4.6 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 85804
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

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

Resolution: 2.3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1160 5 %RANDOM
Rwork0.185 ---
obs0.186 23210 97 %-
all-23210 --
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 4 138 2313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1

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