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- PDB-8djx: Cytosolic ascorbate peroxidase from Sorghum bicolor - Compound II -
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Open data
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Basic information
Entry | Database: PDB / ID: 8djx | |||||||||
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Title | Cytosolic ascorbate peroxidase from Sorghum bicolor - Compound II | |||||||||
![]() | L-ascorbate peroxidase | |||||||||
![]() | OXIDOREDUCTASE / Cytosolic ascorbate peroxidase | |||||||||
Function / homology | ![]() L-ascorbate peroxidase / L-ascorbate peroxidase activity / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, B. / Kang, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A sorghum ascorbate peroxidase with four binding sites has activity against ascorbate and phenylpropanoids. Authors: Zhang, B. / Lewis, J.A. / Vermerris, W. / Sattler, S.E. / Kang, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.6 KB | Display | ![]() |
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PDB format | ![]() | 86.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.7 KB | Display | ![]() |
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Full document | ![]() | 790.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8djrC ![]() 8djsC ![]() 8djtC ![]() 8djuC ![]() 8djwC ![]() 1oagS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 27251.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M Li2SO4, 0.1 M Tris, pH 8.5 and 30 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 31, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.34→41.49 Å / Num. obs: 49922 / % possible obs: 93.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 9.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.029 / Rrim(I) all: 0.072 / Net I/σ(I): 15.3 / Num. measured all: 280527 / Scaling rejects: 14 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OAG Resolution: 1.34→41.49 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 46.41 Å2 / Biso mean: 12.8883 Å2 / Biso min: 4.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.34→41.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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