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- PDB-1cob: CRYSTAL STRUCTURE SOLUTION AND REFINEMENT OF THE SEMISYNTHETIC CO... -

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Entry
Database: PDB / ID: 1cob
TitleCRYSTAL STRUCTURE SOLUTION AND REFINEMENT OF THE SEMISYNTHETIC COBALT SUBSTITUTED BOVINE ERYTHROCYTE ENZYME SUPEROXIDE DISMUTASE AT 2.0 ANGSTROMS RESOLUTION
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity ...neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / 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 / superoxide dismutase / positive regulation of catalytic activity / 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 / regulation of mitochondrial membrane potential / locomotory behavior / 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 / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / 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 / Resolution: 2 Å
AuthorsDjinovic, K. / Coda, A. / Antolini, L. / Pelosi, G. / Desideri, A. / Falconi, M. / Rotilio, G. / Bolognesi, M.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Crystal structure solution and refinement of the semisynthetic cobalt-substituted bovine erythrocyte superoxide dismutase at 2.0 A resolution.
Authors: Djinovic, K. / Coda, A. / Antolini, L. / Pelosi, G. / Desideri, A. / Falconi, M. / Rotilio, G. / Bolognesi, M.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystal Structure of Yeast Cu,Zn Superoxide Dismutase. Crystallographic Refinement at 2.5 Angstroms Resolution
Authors: Djinovic, K. / Gatti, G. / Coda, A. / Antolini, L. / Pelosi, G. / Desideri, A. / Falconi, M. / Marmocchi, F. / Rotilio, G. / Bolognesi, M.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Structure Solution and Molecular Dynamics Refinement of the Yeast Cu,Zn Enzyme Superoxide Dismutase
Authors: Djinovic, K. / Gatti, G. / Coda, A.
#3: Journal: J.Biochem.(Tokyo) / Year: 1991
Title: Three-Dimensional Structure of Cu,Zn Superoxide Dismutase from Spinach at 2.0 Angstroms Resolution
Authors: Kitagawa, Y. / Tanaka, N. / Hata, Y. / Kusonoki, M. / Lee, G. / Katsube, Y. / Asada, K. / Aibara, S. / Morita, Y.
#4: Journal: Proteins / Year: 1989
Title: Evolution of Cu,Zn Superoxide Dismutase and the Greek-Key B-Barrel Structural Motif
Authors: Getzoff, E.D. / Tainer, J.A. / Stempien, M.M. / Bell, G.I. / Hallewell, R.A.
#5: Journal: J.Mol.Biol. / Year: 1982
Title: Determination and Analysis of the 2 Angstroms Structure of Copper, Zinc Superoxide Dismutase
Authors: Tainer, J.A. / Getzoff, E.D. / Beem, K.M. / Richardson, J.S. / Richardson, D.C.
History
DepositionFeb 19, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700SHEET STRAND 4 OF SHEETS SMA AND SMB EXTENDS FROM 141 - 146. ACCORDING TO KABSCH AND SANDER ...SHEET STRAND 4 OF SHEETS SMA AND SMB EXTENDS FROM 141 - 146. ACCORDING TO KABSCH AND SANDER CRITERIA RESIDUE 147 CANNOT BE ATTRIBUTED AN EXTENDED CONFORMATION AND, THEREFORE, THE BETA STRAND IS INTERRUPTED AT THIS SITE. NEVERTHELESS THERE IS A HYDROGEN-BONDING INTERACTION BETWEEN RESIDUES CAL 5 AND GLY 148, AS IF THE BETA STRAND ACTUALLY CONTINUED FOR ONE RESIDUE AFTER 147.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE
B: SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3926
Polymers31,1472
Non-polymers2454
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-37 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.990, 147.630, 47.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES WITH POOR ELECTRON DENSITY: CHAIN A: LYS 3, LYS 9, GLN 15, LYS 23, LYS 73, LYS 89, ASN 90, GLU 107, TYR 108, LYS 120, LYS 151. CHAIN B: LYS 3, ASP 11, LYS 23, ASN 51, LYS 73, LYS 89, GLU 107, LYS 151.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.56818, -0.20434, -0.79713), (-0.22022, -0.9711, 0.09197), (-0.79289, 0.12329, -0.59676)
Vector: 27.526, 119.953, 22.219)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A. THE RMS DEVIATION OF THE CA ATOMS IS 0.282 ANGSTROMS.

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Components

#1: Protein SUPEROXIDE DISMUTASE /


Mass: 15573.337 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00442, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlCu,Co b-SOD1drop
20.050 Mglycylglycine1drop
38 %(w/v)PEG40001drop
40.1 M1dropNaCl
516 %(w/v)PEG1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. obs: 116401 / % possible obs: 75.2 % / Num. measured all: 18964 / Rmerge(I) obs: 0.068

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Processing

Software
NameClassification
TNTrefinement
FRODOmodel building
RefinementResolution: 2→10 Å /
RfactorNum. reflection
obs0.176 18876
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 4 199 2387
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 18876 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg1.748
X-RAY DIFFRACTIONo_dihedral_angle_d26.76
X-RAY DIFFRACTIONo_dihedral_angle_deg
X-RAY DIFFRACTIONo_plane_restr0.014

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