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Yorodumi- PDB-8ff7: Cytosolic ascorbate peroxidase mutant from Panicum virgatum- asco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ff7 | |||||||||
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Title | Cytosolic ascorbate peroxidase mutant from Panicum virgatum- ascorbate complex | |||||||||
Components | Cytosolic ascorbate peroxidase | |||||||||
Keywords | OXIDOREDUCTASE / ascorbate peroxidase / ascorbate / heme / hydrogen peroxide / switchgrass | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Panicum virgatum (switchgrass) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å | |||||||||
Authors | Zhang, B. / Kang, C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Activity of Cytosolic Ascorbate Peroxidase (APX) from Panicum virgatum against Ascorbate and Phenylpropanoids. Authors: Zhang, B. / Lewis, J.A. / Kovacs, F. / Sattler, S.E. / Sarath, G. / Kang, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ff7.cif.gz | 324.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ff7.ent.gz | 264.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ff7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ff7_validation.pdf.gz | 5.4 MB | Display | wwPDB validaton report |
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Full document | 8ff7_full_validation.pdf.gz | 5.5 MB | Display | |
Data in XML | 8ff7_validation.xml.gz | 69.1 KB | Display | |
Data in CIF | 8ff7_validation.cif.gz | 94.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/8ff7 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/8ff7 | HTTPS FTP |
-Related structure data
Related structure data | 8ff6C 8djrS 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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Unit cell |
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-Components
#1: Protein | Mass: 27301.795 Da / Num. of mol.: 6 / Mutation: C4S, E14D, C168A, V221A, K229D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Panicum virgatum (switchgrass) / Gene: PVAP13_9KG480900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T0NWI5 #2: Sugar | ChemComp-ASC / #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | 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: 2.63 Å3/Da / Density % sol: 53.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging 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: 1 Å |
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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.194→49.23 Å / Num. obs: 83162 / % possible obs: 97.17 % / Redundancy: 2.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.1267 / Net I/σ(I): 6.45 |
Reflection shell | Resolution: 2.194→2.273 Å / Redundancy: 7 % / Rmerge(I) obs: 1.54 / Num. unique obs: 7756 / Χ2: -7 / % possible all: 4.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8DJR Resolution: 2.194→49.23 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.31 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.194→49.23 Å
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Refine LS restraints |
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LS refinement shell |
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