[English] 日本語
Yorodumi- PDB-7atj: RECOMBINANT HORSERADISH PEROXIDASE C1A COMPLEX WITH CYANIDE AND F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7atj | ||||||
---|---|---|---|---|---|---|---|
Title | RECOMBINANT HORSERADISH PEROXIDASE C1A COMPLEX WITH CYANIDE AND FERULIC ACID | ||||||
Components | PEROXIDASE C1A | ||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / CYANIDE / FERULIC ACID | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7atj.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7atj.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 7atj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/7atj ftp://data.pdbj.org/pub/pdb/validation_reports/at/7atj | HTTPS FTP |
---|
-Related structure data
Related structure data | 6atjC 1atjS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#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 |
---|
-Non-polymers , 5 types, 446 molecules
#2: Chemical | #3: Chemical | ChemComp-CYN / | #4: Chemical | ChemComp-HEM / | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.015 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1998 / Details: VERTICALLY FOCUSING CYLINDRICAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.015 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→34 Å / Num. obs: 51544 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 1.47→1.5 Å / Rmerge(I) obs: 0.258 / % possible all: 82.7 |
Reflection | *PLUS Num. measured all: 379088 |
Reflection shell | *PLUS % possible obs: 82.7 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ATJ Resolution: 1.47→34 Å / Num. parameters: 11912 / Num. restraintsaints: 10283 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: BULK SOLVENT MODEL USED
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS AND KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 17 / Occupancy sum hydrogen: 2319 / Occupancy sum non hydrogen: 2886 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→34 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.16 / Rfactor Rfree: 0.203 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |