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Yorodumi- PDB-4o79: Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o79 | ||||||
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Title | Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes | ||||||
Components | Probable transmembrane ascorbate ferrireductase 2 | ||||||
Keywords | OXIDOREDUCTASE / alpha helical membrane protein / ascorbate-dependent oxidoreductase | ||||||
Function / homology | Function and homology information ferric-chelate reductase activity / ascorbate ferrireductase (transmembrane) / transmembrane ascorbate ferrireductase activity / L-ascorbic acid metabolic process / Golgi apparatus / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å | ||||||
Authors | Lu, P. / Ma, D. / Yan, C. / Gong, X. / Du, M. / Shi, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structure and mechanism of a eukaryotic transmembrane ascorbate-dependent oxidoreductase Authors: Lu, P. / Ma, D. / Yan, C. / Gong, X. / Du, M. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o79.cif.gz | 187.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o79.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 4o79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o79_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4o79_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4o79_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 4o79_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/4o79 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/4o79 | HTTPS FTP |
-Related structure data
Related structure data | 4o6ySC 4o7gC 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
#1: Protein | Mass: 25310.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYB561B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SWS1, EC: 1.16.5.1 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-SO4 / | #4: Sugar | ChemComp-ASC / | #5: Water | ChemComp-HOH / | |
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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: 2.19 Å3/Da / Density % sol: 43.77 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% PEG400, 400mM Li2SO4, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 30170 / Num. obs: 29506 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 33.72 Å2 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4O6Y Resolution: 2.003→30.585 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8514 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 21.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.63 Å2 / Biso mean: 43.8759 Å2 / Biso min: 22.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.003→30.585 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: 12.4521 Å / Origin y: 24.2453 Å / Origin z: -23.5938 Å
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Refinement TLS group | Selection details: ALL |