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Yorodumi- PDB-1itk: Crystal structure of catalase-peroxidase from Haloarcula marismortui -
+Open data
-Basic information
Entry | Database: PDB / ID: 1itk | ||||||
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Title | Crystal structure of catalase-peroxidase from Haloarcula marismortui | ||||||
Components | catalase-peroxidase | ||||||
Keywords | OXIDOREDUCTASE / HEME PROTEIN | ||||||
Function / homology | Function and homology information catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Yamada, Y. / Fujiwara, T. / Sato, T. / Igarashi, N. / Tanaka, N. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: The 2.0 A crystal structure of catalase-peroxidase from Haloarcula marismortui. Authors: Yamada, Y. / Fujiwara, T. / Sato, T. / Igarashi, N. / Tanaka, N. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1itk.cif.gz | 318.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1itk.ent.gz | 253.7 KB | Display | PDB format |
PDBx/mmJSON format | 1itk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/1itk ftp://data.pdbj.org/pub/pdb/validation_reports/it/1itk | 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 81460.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: O59651, catalase |
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-Non-polymers , 5 types, 1405 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-UNX / #5: Chemical | #6: 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: 2.96 Å3/Da / Density % sol: 58.41 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, potassium chloride, Tris/HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2001 / Details: mirrors |
Radiation | Monochromator: silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→34 Å / Num. all: 128391 / Num. obs: 128391 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5 / Num. unique all: 18662 / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 34.1 Å / Num. measured all: 479060 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 99.7 % / Num. unique obs: 18662 / Num. measured obs: 67473 / Rmerge(I) obs: 0.14 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→34.1 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.098 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→34.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.205 / Rfactor Rwork: 0.185 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.2378 / Rfactor Rwork: 0.2137 |