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Yorodumi- PDB-2atj: RECOMBINANT HORSERADISH PEROXIDASE COMPLEX WITH BENZHYDROXAMIC ACID -
+Open data
-Basic information
Entry | Database: PDB / ID: 2atj | ||||||
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Title | RECOMBINANT HORSERADISH PEROXIDASE 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 Å | ||||||
Authors | Henriksen, A. / Schuller, D.J. / Gajhede, M. | ||||||
Citation | 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. #1: 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. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Crystallization and Preliminary X-Ray Studies of Recombinant Horseradish Peroxidase Authors: Henriksen, A. / Gajhede, M. / Baker, P. / Smith, A.T. / Burke, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2atj.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2atj.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 2atj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/2atj ftp://data.pdbj.org/pub/pdb/validation_reports/at/2atj | HTTPS FTP |
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-Related structure data
Related structure data | 1schS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, -0.0063, 0.0026), Vector: |
-Components
#1: Protein | Mass: 33992.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Armoracia rusticana (horseradish) / Production host: Escherichia coli (E. coli) / References: UniProt: P00433, peroxidase #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: 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: 2.59 Å3/Da / Density % sol: 52.51 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 283 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1995 |
Radiation | Monochromator: GRAPHITE(002) / 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: 46595 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.085 |
Reflection shell | Resolution: 2→2.1 Å / % possible all: 92.8 |
Reflection | *PLUS Num. measured all: 144839 |
Reflection shell | *PLUS % possible obs: 92.8 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SCH Resolution: 2→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: A BULK SOLVENT MODEL USED. THE STRUCTURE WAS REFINED USING STRICT NON- CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS.
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Displacement parameters | Biso mean: 14.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 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→2.09 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 28.6 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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