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Open data
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Basic information
Entry | Database: PDB / ID: 3b6i | ||||||
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Title | WrbA from Escherichia coli, native structure | ||||||
![]() | Flavoprotein wrbA | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Andrade, S.L.A. / Patridge, E.V. / Ferry, J.G. / Einsle, O. | ||||||
![]() | ![]() Title: Crystal structure of the NADH:quinone oxidoreductase WrbA from Escherichia coli. Authors: Andrade, S.L. / Patridge, E.V. / Ferry, J.G. / Einsle, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.3 KB | Display | ![]() |
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PDB format | ![]() | 77.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3b6jC ![]() 3b6kC ![]() 3b6mC ![]() 1ydgS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 20862.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-15P / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.68 Å3/Da / Density % sol: 73.71 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 15-35 % PEG 1500, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 2006 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.66→50 Å / Num. all: 92983 / Num. obs: 91774 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rsym value: 0.12 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.68 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1YDG Resolution: 1.66→29.41 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.403 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.749 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→29.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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