+Open data
-Basic information
Entry | Database: PDB / ID: 6atj | ||||||
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Title | RECOMBINANT HORSERADISH PEROXIDASE C COMPLEX WITH FERULIC ACID | ||||||
Components | PEROXIDASE C1A | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / REDUCING SUBSTRATE | ||||||
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. / Smith, A.T. / Gajhede, M. | ||||||
Citation | 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. #1: 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. #2: 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. #3: 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 | 6atj.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6atj.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 6atj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/6atj ftp://data.pdbj.org/pub/pdb/validation_reports/at/6atj | HTTPS FTP |
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-Related structure data
Related structure data | 7atjC 1atjS 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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Unit cell |
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-Components
#1: Protein | Mass: 33948.141 Da / Num. of mol.: 1 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 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-FER / | #5: Water | ChemComp-HOH / | Sequence details | THE SWS ENTRY INCLUDES N-TERM AND C-TERM SIGNAL PEPTIDES. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.5 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 16% (W/V) PEG 4000, 0.2 M CALCIUM ACETATE AND 0.1 M CACODYLATE BUFFER, PH 6.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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 / Detector: IMAGE PLATE / Date: Jul 1, 1995 |
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→29 Å / Num. obs: 21778 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 2.9 Å2 / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.208 / % possible all: 96 |
Reflection | *PLUS % possible obs: 97.2 % / Num. measured all: 108409 |
Reflection shell | *PLUS % possible obs: 96 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ATJ Resolution: 2→29 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 344924.86 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 21751 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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