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Yorodumi- PDB-8djs: Cytosolic ascorbate peroxidase from Sorghum bicolor - one ascorba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8djs | |||||||||
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Title | Cytosolic ascorbate peroxidase from Sorghum bicolor - one ascorbate complex | |||||||||
Components | L-ascorbate peroxidase | |||||||||
Keywords | OXIDOREDUCTASE / Cytosolic ascorbate peroxidase | |||||||||
Function / homology | Function and homology information 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 | Sorghum bicolor (sorghum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | |||||||||
Authors | Zhang, B. / Kang, C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Plant Physiol. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8djs.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8djs.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 8djs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8djs_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8djs_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8djs_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8djs_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/8djs ftp://data.pdbj.org/pub/pdb/validation_reports/dj/8djs | HTTPS FTP |
-Related structure data
Related structure data | 8djrC 8djtC 8djuC 8djwC 8djxC 1oagS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 27251.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: SORBI_3001G410200 / Production host: Escherichia coli (E. coli) / References: UniProt: C5WNL8, L-ascorbate peroxidase |
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#3: Sugar | ChemComp-ASC / |
-Non-polymers , 4 types, 331 molecules
#2: Chemical | ChemComp-HEM / |
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#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.31 % |
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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: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 22, 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: 1.19→41.48 Å / Num. obs: 72524 / % possible obs: 94.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 9.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.033 / Rrim(I) all: 0.082 / Net I/σ(I): 13 / Num. measured all: 418318 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OAG Resolution: 1.19→41.48 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.84 / 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: 48.81 Å2 / Biso mean: 13.6237 Å2 / Biso min: 5.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.19→41.48 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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