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Yorodumi- PDB-1ck6: BINDING MODE OF SALICYLHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PER... -
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-Basic information
Entry | Database: PDB / ID: 1ck6 | |||||||||
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Title | BINDING MODE OF SALICYLHYDROXAMIC ACID 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: 1.9 Å | |||||||||
Authors | Fukuyama, K. / Itakura, H. | |||||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Binding of salicylhydroxamic acid and several aromatic donor molecules to Arthromyces ramosus peroxidase, investigated by X-ray crystallography, optical difference spectroscopy, NMR ...Title: Binding of salicylhydroxamic acid and several aromatic donor molecules to Arthromyces ramosus peroxidase, investigated by X-ray crystallography, optical difference spectroscopy, NMR relaxation, molecular dynamics, and kinetics. Authors: Tsukamoto, K. / Itakura, H. / Sato, K. / Fukuyama, K. / Miura, S. / Takahashi, S. / Ikezawa, H. / Hosoya, T. #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 | 1ck6.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ck6.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ck6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ck6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1ck6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1ck6_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1ck6_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/1ck6 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/1ck6 | HTTPS FTP |
-Related structure data
Related structure data | 1arpS 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, 211 molecules
#4: Chemical | #5: Chemical | ChemComp-SHA / | #6: Chemical | ChemComp-HEM / | #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: 2.26 Å3/Da / Density % sol: 45.67 % Description: DATA WERE COLLECTED ON R-AXIS IV WITH CRYSTAL-IP DISTANCE OF 120 MM. | ||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | ||||||||||||||||||||
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 | 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 / 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: 1.9→50 Å / Num. obs: 24996 / % possible obs: 93.5 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.195 / % possible all: 92 |
Reflection | *PLUS Num. measured all: 119252 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1ARP Resolution: 1.9→7 Å / Isotropic thermal model: RESTRAINED / σ(F): 2 / Details: RMSD BOND ANGLE DISTANCES 0.051 ANGSTROMS
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Refinement step | Cycle: LAST / Resolution: 1.9→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 Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.163 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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