+Open data
-Basic information
Entry | Database: PDB / ID: 1c8i | |||||||||
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Title | BINDING MODE OF HYDROXYLAMINE TO ARTHROMYCES RAMOSUS PEROXIDASE | |||||||||
Components | PROTEIN (PEROXIDASE) | |||||||||
Keywords | OXIDOREDUCTASE / GLYCOPROTEIN / PEROXIDASE | |||||||||
Function / homology | Function and homology information lactoperoxidase activity / peroxidase / response to reactive oxygen species / 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 / OTHER / Resolution: 2 Å | |||||||||
Authors | Wariishi, H. / Nonaka, D. / Johjima, T. / Nakamura, N. / Naruta, Y. / Kubo, K. / Fukuyama, K. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Direct binding of hydroxylamine to the heme iron of Arthromyces ramosus peroxidase. Substrate analogue that inhibits compound I formation in a competetive manner. Authors: Wariishi, H. / Nonaka, D. / Johjima, T. / Nakamura, N. / Naruta, Y. / Kubo, S. / Fukuyama, K. #1: 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. #2: 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. #3: 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. #4: 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. #5: 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. #6: 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 | 1c8i.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c8i.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 1c8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/1c8i ftp://data.pdbj.org/pub/pdb/validation_reports/c8/1c8i | HTTPS FTP |
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-Related structure data
Related structure data | 1gzbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 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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-Sugars , 2 types, 2 molecules
#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 |
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#3: Sugar | ChemComp-BMA / |
-Non-polymers , 4 types, 212 molecules
#4: Chemical | #5: Chemical | ChemComp-HEM / | #6: Chemical | ChemComp-HOA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.91 % Description: DATA WERE COLLECTED ON R-AXIS IV WITH CRYSTAL-IP DISTANCE OF 120 MM. | ||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: pH 5.6 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22-24 ℃ / pH: 7.5 / Method: vapor diffusion, hanging dropDetails: used seeding, Kunishima, N., (1993) Proteins: Struct., Funct., Genet., 15, 216. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Aug 15, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 21938 / % possible obs: 94.2 % / Observed criterion σ(I): 1 / Redundancy: 4.94 % / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 2→2.25 Å / Rmerge(I) obs: 0.177 / % possible all: 90.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Observed criterion σ(I): 1 / Num. measured all: 108471 |
Reflection shell | *PLUS % possible obs: 90.6 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1GZB Resolution: 2→7 Å / Isotropic thermal model: RESTRAINED / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→7 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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