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- PDB-7atj: RECOMBINANT HORSERADISH PEROXIDASE C1A COMPLEX WITH CYANIDE AND F... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7atj | ||||||
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Title | RECOMBINANT HORSERADISH PEROXIDASE C1A COMPLEX WITH CYANIDE AND FERULIC ACID | ||||||
![]() | PEROXIDASE C1A | ||||||
![]() | OXIDOREDUCTASE / PEROXIDASE / CYANIDE / FERULIC ACID | ||||||
Function / homology | ![]() lactoperoxidase activity / peroxidase / vacuole / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Henriksen, A. / Smith, A.T. / Gajhede, M. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.6 KB | Display | ![]() |
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PDB format | ![]() | 91.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 784.6 KB | Display | ![]() |
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Full document | ![]() | 788.4 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6atjC ![]() 1atjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 446 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/FER.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/FER.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CYN / | #4: Chemical | ChemComp-HEM / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SWS ENTRY INCLUDES N-TERM AND C-TERM SIGNAL PEPTIDES. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % | ||||||||||||||||||||||||
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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: ![]() ![]() ![]() |
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 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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
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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
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.16 / Rfactor Rfree: 0.203 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |