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Yorodumi- PDB-1hsr: BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hsr | |||||||||
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Title | BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE | |||||||||
Components | PEROXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / GLYCOPROTEIN / PEROXIDASE | |||||||||
Function / homology | Function and homology information lactoperoxidase activity / peroxidase / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | 'Arthromyces ramosus' (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | |||||||||
Authors | Fukuyama, K. / Itakura, H. | |||||||||
Citation | Journal: FEBS Lett. / Year: 1997 Title: Binding mode of benzhydroxamic acid to Arthromyces ramosus peroxidase shown by X-ray crystallographic analysis of the complex at 1.6 A resolution. Authors: Itakura, H. / Oda, Y. / Fukuyama, K. #1: Journal: J.Biol.Chem. / Year: 1997 Title: Binding of Iodide to Arthromyces Ramosus Peroxidase Investigated with X-Ray Crystallographic Analysis, 1H and 127I NMR Spectroscopy, and Steady-State Kinetics Authors: Fukuyama, K. / Sato, K. / Itakura, H. / Takahashi, S. / Hosoya, T. #2: Journal: FEBS Lett. / Year: 1996 Title: Pentacoordination of the Heme Iron of Arthromyces Ramosus Peroxidase Shown by a 1.8 A Resolution Crystallographic Study at Ph 4.5 Authors: Kunishima, N. / Amada, F. / Fukuyama, K. / Kawamoto, M. / Matsunaga, T. / Matsubara, H. #3: Journal: J.Biol.Chem. / Year: 1995 Title: Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different Ph Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis Authors: Fukuyama, K. / Kunishima, N. / Amada, F. / Kubota, T. / Matsubara, H. #4: Journal: J.Mol.Biol. / Year: 1994 Title: Crystal Structure of the Fungal Peroxidase from Arthromyces Ramosus at 1.9 A Resolution. Structural Comparisons with the Lignin and Cytochrome C Peroxidases Authors: Kunishima, N. / Fukuyama, K. / Matsubara, H. / Hatanaka, H. / Shibano, Y. / Amachi, T. #5: Journal: Proteins / Year: 1993 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Peroxidase from a Fungus Arthromyces Ramosus Authors: Kunishima, N. / Fukuyama, K. / Wakabayashi, S. / Sumida, M. / Takaya, M. / Shibano, Y. / Amachi, T. / Matsubara, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hsr.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hsr.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 1hsr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/1hsr ftp://data.pdbj.org/pub/pdb/validation_reports/hs/1hsr | HTTPS FTP |
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-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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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 35722.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 'Arthromyces ramosus' (fungus) / Genus: 'Arthromyces' / References: UniProt: P28313, peroxidase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 245 molecules
#3: Chemical | #4: Chemical | ChemComp-HEM / | #5: Chemical | ChemComp-BHO / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46 % Description: DATA WERE COLLECTED ON A WEISSENBERG CAMERA USING A CYLINDRICAL CASSETTE HAVING A 287 MM RADIUS. | ||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22-24 ℃ / pH: 7.5 / Method: vapor diffusion, hanging dropDetails: repeated seeding, Kunishima, N., (1993) Proteins: Struct.,Funct., Genet., 15, 216. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
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Detector | Type: FUJI / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. obs: 47193 / % possible obs: 87.6 % / Num. measured all: 225152 / Rmerge(I) obs: 0.047 |
-Processing
Software |
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Refinement | Resolution: 1.6→7 Å / Rfactor Rwork: 0.187 / Rfactor obs: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→7 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 39924 / σ(F): 2 / Rfactor Rfree: 0.227 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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