[English] 日本語
Yorodumi- PDB-4o7g: Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o7g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 40 minutes | ||||||
Components | Probable transmembrane ascorbate ferrireductase 2 | ||||||
Keywords | OXIDOREDUCTASE / alpha helical transmembrane protein / ascorbate-dependent oxidoreductase | ||||||
Function / homology | Function and homology information ascorbate ferrireductase (transmembrane) / ferric-chelate reductase activity / 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: 2.211 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4o7g.cif.gz | 188.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4o7g.ent.gz | 152.2 KB | Display | PDB format |
PDBx/mmJSON format | 4o7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/4o7g ftp://data.pdbj.org/pub/pdb/validation_reports/o7/4o7g | HTTPS FTP |
---|
-Related structure data
Related structure data | 4o6ySC 4o79C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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: Sugar | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% PEG400, 400mM Li2SO4, 100mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.2→40 Å / Num. all: 22486 / Num. obs: 22284 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 43.13 Å2 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4O6Y Resolution: 2.211→28.077 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8221 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 24.37 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.338 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.47 Å2 / Biso mean: 54.571 Å2 / Biso min: 20 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.211→28.077 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -12.5677 Å / Origin y: 24.3184 Å / Origin z: 23.3703 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |