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Yorodumi- PDB-1h3j: STRUCTURE OF RECOMBINANT COPRINUS CINEREUS PEROXIDASE DETERMINED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h3j | ||||||||||||
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Title | STRUCTURE OF RECOMBINANT COPRINUS CINEREUS PEROXIDASE DETERMINED TO 2.0 A | ||||||||||||
Components | Peroxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / HEME / CALCIUM-BINDING | ||||||||||||
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 | Coprinopsis cinerea (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Petersen, J.F.W. / Houborg, K. / Harris, P. / Larsen, S. | ||||||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Impact of the Physical and Chemical Environment on the Molecular Structure of Coprinus Cinereus Peroxidase Authors: Houborg, K. / Harris, P. / Petersen, J.F.W. / Rowland, P. / Poulsen, J. / Schneider, P. / Vind, J. / Larsen, S. #1: Journal: FEBS Lett. / Year: 1994 Title: Three-Dimensional Structure of a Recombinant Peroxidase from Coprinus Cinereus at 2.6 A Authors: Petersen, J.F.W. / Kadziola, A. / Larsen, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h3j.cif.gz | 147.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h3j.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/1h3j ftp://data.pdbj.org/pub/pdb/validation_reports/h3/1h3j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35523.590 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 22-363 Source method: isolated from a genetically manipulated source Details: N-LINKED GLYCOSYLATION SITE AT ASN142 O-LINKED GLYCOSYLATION SITE AT SER338 Source: (gene. exp.) Coprinopsis cinerea (fungus) / Gene: CIP1 / Production host: ASPERGILLUS ORYZAE (mold) / References: UniProt: P28314, peroxidase |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 4 types, 505 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ACTIVITY INVOLVES DONOR + H(2)O(2) = OXIDIZED DONOR + 2 H(2)O. USALLY OCCURS BOUND TO PROTOHEME IX, ...ACTIVITY INVOLVES DONOR + H(2)O(2) = OXIDIZED DONOR + 2 H(2)O. USALLY OCCURS BOUND TO PROTOHEME IX, IRON(III) ION AND 2 CALCIUM IONS PER SUBUNIT. N-LINKED GLYCOSYLAT |
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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: 2.59 Å3/Da / Density % sol: 52.52 % |
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Crystal grow | pH: 7 / Details: 18% PEG6000, 0.35 M MGCL2, 0.1 M HEPES, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
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→30 Å / Num. obs: 50569 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.209 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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