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- PDB-1oaf: Ascobate peroxidase from soybean cytosol in complex with ascorbate -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oaf | ||||||
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Title | Ascobate peroxidase from soybean cytosol in complex with ascorbate | ||||||
![]() | ASCORBATE PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / HEME PEROXIDASE / PEROXIDE SCAVENGE / ASCORBATE PEROXIDASE | ||||||
Function / homology | ![]() L-ascorbate peroxidase / L-ascorbate peroxidase activity / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharp, K.H. / Raven, E.L. / Moody, P.C.E. | ||||||
![]() | ![]() Title: Crystal Structure of the Ascorbate Peroxidase-Ascorbate Complex Authors: Sharp, K.H. / Mewies, M. / Moody, P.C.E. / Raven, E.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.6 KB | Display | ![]() |
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PDB format | ![]() | 101.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 828.1 KB | Display | ![]() |
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Full document | ![]() | 832.8 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1oagC ![]() 1apxS 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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Unit cell |
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Components
#1: Protein | Mass: 28361.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NA / |
#4: Sugar | ChemComp-ASC / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8.3 / Details: 2.25M LI2SO4, 0.1M HEPES, PH8.3, pH 8.30 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→54 Å / Num. obs: 49370 / % possible obs: 96.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.4→1.44 Å / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.9 / % possible all: 96.2 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 57.74 Å / Num. measured all: 339792 |
Reflection shell | *PLUS Highest resolution: 1.4 Å / % possible obs: 96.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1APX Resolution: 1.4→57.74 Å / SU B: 0.886 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.065 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUE 1 AND THE N-TERMINAL HIS-TAG ARE NOT VISIBLE
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Displacement parameters | Biso mean: 15.671 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→57.74 Å
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Refinement | *PLUS Highest resolution: 1.4 Å / Rfactor Rfree: 0.214 / Rfactor Rwork: 0.196 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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