+Open data
-Basic information
Entry | Database: PDB / ID: 6ky4 | ||||||
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Title | Crystal structure of Sulfiredoxin from Arabidopsis thaliana | ||||||
Components | Sulfiredoxin, chloroplastic/mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / sulfiredoxin / cysteine / sulfinic acid / peroxiredoxin repair protein / arabidopsis thaliana / antioxidant | ||||||
Function / homology | Function and homology information sulfiredoxin / sulfiredoxin activity / chloroplast / cellular response to oxidative stress / mitochondrion / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Liu, M. / Wang, J. / Li, X. / Li, M. / Sylvanno, M.J. / Zhang, M. / Wang, M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: The crystal structure of sulfiredoxin from Arabidopsis thaliana revealed a more robust antioxidant mechanism in plants. Authors: Liu, M. / Wang, J. / Li, X. / Sylvanno, M.J. / Li, M. / Zhang, M. / Wang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ky4.cif.gz | 34.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ky4.ent.gz | 21.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ky4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ky4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ky4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ky4_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 6ky4_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/6ky4 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/6ky4 | HTTPS FTP |
-Related structure data
Related structure data | 1xw3S S: Starting model for refinement |
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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
#1: Protein | Mass: 12769.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SRX, At1g31170, F28K20.12 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8GY89, sulfiredoxin | ||||
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#2: Chemical | ChemComp-ADP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.04 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.8 M NaH2PO4/1.2 M KH2PO4, acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 3377 / % possible obs: 99.9 % / Redundancy: 37 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.018 / Rrim(I) all: 0.099 / Χ2: 1.054 / Net I/σ(I): 12 / Num. measured all: 124863 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1xw3 Resolution: 3.2→41.863 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 104.52 Å2 / Biso mean: 66.2696 Å2 / Biso min: 38.51 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→41.863 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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