+Open data
-Basic information
Entry | Database: PDB / ID: 8cat | ||||||||||||
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Title | The NADPH binding site on beef liver catalase | ||||||||||||
Components | CATALASE | ||||||||||||
Keywords | OXIDOREDUCTASE / H2O2 ACCEPTOR | ||||||||||||
Function / homology | Function and homology information Detoxification of Reactive Oxygen Species / catalase complex / cellular detoxification of hydrogen peroxide / Peroxisomal protein import / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide ...Detoxification of Reactive Oxygen Species / catalase complex / cellular detoxification of hydrogen peroxide / Peroxisomal protein import / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / enzyme binding / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||||||||
Authors | Murthy, M.R.N. / Reid III, T.J. / Sicignano, A. / Tanaka, N. / Fita, I. / Rossmann, M.G. | ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1985 Title: The NADPH binding site on beef liver catalase. Authors: Fita, I. / Rossmann, M.G. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1986 Title: The Refined Structure of Beef Liver Catalase at 2.5 Angstroms Resolution Authors: Fita, I. / Silva, A.M. / Murthy, M.R.N. / Rossmann, M.G. #2: Journal: J.Mol.Biol. / Year: 1986 Title: Comparison of Beef Liver and Penicillium Vitale Catalases Authors: Melik-Adamyan, W.R. / Barynin, V.V. / Vagin, A.A. / Borisov, V.V. / Vainshtein, B.K. / Fita, I. / Murthy, M.R.N. / Rossmann, M.G. #3: Journal: J.Mol.Biol. / Year: 1985 Title: The Active Center of Catalase Authors: Fita, I. / Rossmann, M.G. #4: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of Beef Liver Catalase Authors: Murthy, M.R.N. / Reid III, T.J. / Sicignano, A. / Tanaka, N. / Rossmann, M.G. #5: Journal: Kristallografiya / Year: 1981 Title: The Structure of Beef Liver Catalase Authors: Murthy, M.R.N. / Reid III, T.J. / Sicignano, A. / Tanaka, N. / Rossmann, M.G. #6: Journal: Sov.Phys.Crystallogr.(Engl.Transl.) / Year: 1981 Title: The Structure of Beef Liver Catalase Authors: Murthy, M.R.N. / Reid III, T.J. / Sicignano, A. / Tanaka, N. / Rossmann, M.G. #7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981 Title: Structure and Heme Environment of Beef Liver Catalase at 2.5 Angstroms Resolution Authors: Reid III, T.J. / Murthy, M.R.N. / Sicignano, A. / Tanaka, N. / Musick, W.D.L. / Rossmann, M.G. #8: Journal: J.Mol.Biol. / Year: 1976 Title: Crystalline Bovine Liver Catalase Authors: Eventoff, W. / Tanaka, N. / Rossmann, M.G. #9: Journal: J.Mol.Biol. / Year: 1975 Title: The Molecular Symmetry of Bovine Liver Catalase Authors: Eventoff, W. / Gurskaya, G.V. | ||||||||||||
History |
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Remark 700 | SHEET THE NINE-STRANDED SHEETS S1A AND S1B DESCRIBED BELOW ARE ACTUALLY EIGHT-STRANDED BETA BARRELS. ...SHEET THE NINE-STRANDED SHEETS S1A AND S1B DESCRIBED BELOW ARE ACTUALLY EIGHT-STRANDED BETA BARRELS. THIS IS DENOTED BY THE FIRST STRAND RECURRING AS THE LAST STRAND. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cat.cif.gz | 219.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cat.ent.gz | 171.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/8cat ftp://data.pdbj.org/pub/pdb/validation_reports/ca/8cat | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUE 405 IS A CIS-PROLINE. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.918275, 0.047185, -0.393099), Vector: Details | Translation is required to obtain the tetramer because the coordinates are not presented in standard frame. | |
-Components
#1: Protein | Mass: 57664.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00432, catalase #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: 2.62 Å3/Da / Density % sol: 52.97 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.8 / Method: unknownDetails: referred to 'Reid /III, T.J.', (1981) Proc.Nat.Acad.Sci.USA, 78, 4767-4771 | ||||||||||||||||||||||||
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 |
-Processing
Refinement | Resolution: 2.5→8.5 Å / Rfactor Rwork: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement step | Cycle: LAST / Resolution: 2.5→8.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8.5 Å / Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |