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Yorodumi- PDB-7bi1: XFEL crystal structure of soybean ascorbate peroxidase compound II -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bi1 | ||||||
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Title | XFEL crystal structure of soybean ascorbate peroxidase compound II | ||||||
Components | Ascorbate peroxidase | ||||||
Keywords | OXIDOREDUCTASE / Intermediates / Heme protein | ||||||
Function / homology | Function and homology information 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 | Glycine max (soybean) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kwon, H. / Tosha, T. / Sugimoto, H. / Raven, E.L. / Moody, P.C.E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: XFEL Crystal Structures of Peroxidase Compound II. Authors: Kwon, H. / Basran, J. / Pathak, C. / Hussain, M. / Freeman, S.L. / Fielding, A.J. / Bailey, A.J. / Stefanou, N. / Sparkes, H.A. / Tosha, T. / Yamashita, K. / Hirata, K. / Murakami, H. / ...Authors: Kwon, H. / Basran, J. / Pathak, C. / Hussain, M. / Freeman, S.L. / Fielding, A.J. / Bailey, A.J. / Stefanou, N. / Sparkes, H.A. / Tosha, T. / Yamashita, K. / Hirata, K. / Murakami, H. / Ueno, G. / Ago, H. / Tono, K. / Yamamoto, M. / Sawai, H. / Shiro, Y. / Sugimoto, H. / Raven, E.L. / Moody, P.C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bi1.cif.gz | 125.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bi1.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 7bi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bi1_validation.pdf.gz | 798.3 KB | Display | wwPDB validaton report |
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Full document | 7bi1_full_validation.pdf.gz | 801.3 KB | Display | |
Data in XML | 7bi1_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 7bi1_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/7bi1 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/7bi1 | HTTPS FTP |
-Related structure data
Related structure data | 7biuC 5jprS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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.) Glycine max (soybean) / Gene: apx1, GLYMA_U021900 / Production host: Escherichia coli (E. coli) / References: UniProt: Q43758, L-ascorbate peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-K / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.25 M Lithium sulfate, 0.1 M HEPES pH 8.3 - 8.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→58 Å / Num. obs: 41508 / % possible obs: 100 % / Redundancy: 662 % / CC1/2: 0.98 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.5→1.51 Å / Num. unique obs: 8746 / CC1/2: 0.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JPR Resolution: 1.5→58 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 114.46 Å2 / Biso mean: 31.6152 Å2 / Biso min: 16.57 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→58 Å
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