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Yorodumi- PDB-1cob: CRYSTAL STRUCTURE SOLUTION AND REFINEMENT OF THE SEMISYNTHETIC CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cob | ||||||
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Title | CRYSTAL STRUCTURE SOLUTION AND REFINEMENT OF THE SEMISYNTHETIC COBALT SUBSTITUTED BOVINE ERYTHROCYTE ENZYME SUPEROXIDE DISMUTASE AT 2.0 ANGSTROMS RESOLUTION | ||||||
Components | SUPEROXIDE DISMUTASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information Platelet degranulation / Detoxification of Reactive Oxygen Species / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / regulation of protein kinase activity / retina homeostasis / negative regulation of cholesterol biosynthetic process ...Platelet degranulation / Detoxification of Reactive Oxygen Species / neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / regulation of protein kinase activity / retina homeostasis / negative regulation of cholesterol biosynthetic process / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / positive regulation of catalytic activity / muscle cell cellular homeostasis / heart contraction / superoxide metabolic process / superoxide dismutase / transmission of nerve impulse / superoxide dismutase activity / : / 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 / regulation of mitochondrial membrane potential / positive regulation of cytokine production / locomotory behavior / sensory perception of sound / regulation of blood pressure / response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / peroxisome / protein-folding chaperone binding / response to heat / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Djinovic, 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 |
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Remark 700 | SHEET 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cob.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cob.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cob_validation.pdf.gz | 429.3 KB | Display | wwPDB validaton report |
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Full document | 1cob_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 1cob_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1cob_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/1cob ftp://data.pdbj.org/pub/pdb/validation_reports/co/1cob | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: 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), Vector: Details | THE 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. | |
-Components
#1: Protein | 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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative 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 |
-Processing
Software |
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Refinement | Resolution: 2→10 Å /
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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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
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