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Yorodumi- PDB-1gx2: Recombinant horseradish peroxidase Phe209Ser complex with benzhyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gx2 | ||||||
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Title | Recombinant horseradish peroxidase Phe209Ser complex with benzhydroxamic acid | ||||||
Components | PEROXIDASE C1A | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE | ||||||
Function / homology | Function and homology information lactoperoxidase activity / peroxidase / vacuole / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ARMORACIA RUSTICANA (horseradish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Meno, K. / Gajhede, M. / Henriksen, A. | ||||||
Citation | Journal: To be Published Title: Hrpc Heme Crevice Architecture Authors: Henriksen, A. / Brissett, N. / Meno, K. / Mirza, O. / Gajhede, M. #1: Journal: J.Biol.Chem. / Year: 1999 Title: The Structures of the Horseradish Peroxidase C-Ferulic Acid Complex and the Ternary Complex with Cyanide Suggest How Peroxidases Oxidize Small Phenolic Substrates Authors: Henriksen, A. / Smith, A.T. / Gajhede, M. #2: Journal: Biochemistry / Year: 1998 Title: Structural Interactions between Horseradish Peroxidase C and the Substrate Benzhydroxamic Acid Determined by X-Ray Crystallography Authors: Henriksen, A. / Schuller, D.J. / Meno, K. / Welinder, K.G. / Smith, A.T. / Gajhede, M. #3: Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal Structure of Horseradish Peroxidase C at 2.15 A Resolution Authors: Gajhede, M. / Schuller, D.J. / Henriksen, A. / Smith, A.T. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gx2.cif.gz | 142.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gx2.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/1gx2 ftp://data.pdbj.org/pub/pdb/validation_reports/gx/1gx2 | HTTPS FTP |
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-Related structure data
Related structure data | 1gw2C 1gwoC 1gwtC 1gwuC 2atjS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34019.246 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARMORACIA RUSTICANA (horseradish) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00433, peroxidase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.6 Å3/Da / Density % sol: 52.78 % |
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Crystal grow | pH: 6.5 / Details: pH 6.50 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 15, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.92 Å / Num. obs: 113464 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 4.7 Å2 / Rmerge(I) obs: 0.106 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.391 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ATJ Resolution: 2.2→37.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 12108 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.4833 Å2 / ksol: 0.339209 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→37.92 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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