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Yorodumi- PDB-3vnw: Crystal structure of cytochrome c552 from Thermus thermophilus at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vnw | ||||||
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Title | Crystal structure of cytochrome c552 from Thermus thermophilus at pH 5.44 | ||||||
Components | Cytochrome c-552 | ||||||
Keywords | ELECTRON TRANSPORT / Cytochrome c / Electron Transfer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Yamada, S. / Bouley-Ford, N.D. / Keller, G.E. / Winkler, J.R. / Gray, H.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Snapshots of a protein folding intermediate Authors: Yamada, S. / Bouley-Ford, N.D. / Keller, G.E. / Ford, W.C. / Gray, H.B. / Winkler, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vnw.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vnw.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vnw_validation.pdf.gz | 803.4 KB | Display | wwPDB validaton report |
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Full document | 3vnw_full_validation.pdf.gz | 805.2 KB | Display | |
Data in XML | 3vnw_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 3vnw_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/3vnw ftp://data.pdbj.org/pub/pdb/validation_reports/vn/3vnw | HTTPS FTP |
-Related structure data
Related structure data | 1dt1S 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: 13995.368 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cycA / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04164 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.44 Details: 0.2M Imidazole-Malate, 42% MPEG 5K, pH 5.44, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→25.68 Å / Num. all: 9951 / Num. obs: 9814 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.6 / Num. unique all: 956 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DT1 Resolution: 1.97→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.903 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.245 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
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