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Open data
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Basic information
Entry | Database: PDB / ID: 3wr8 | ||||||
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Title | Crystal structure of DesB from Sphingobium sp. strain SYK-6 | ||||||
![]() | Gallate dioxygenase![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugimoto, K. / Senda, M. / Kasai, D. / Fukuda, M. / Masai, E. / Senda, T. | ||||||
![]() | ![]() Title: Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6 Authors: Sugimoto, K. / Senda, M. / Kasai, D. / Fukuda, M. / Masai, E. / Senda, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.1 KB | Display | ![]() |
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PDB format | ![]() | 137.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3wkuC ![]() 3wpmC ![]() 3wr3C ![]() 3wr4C ![]() 3wr9C ![]() 3wraC ![]() 3wrbC ![]() 3wrcC ![]() 1bouS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 46953.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q5NTE5, UniProt: G2IKE5*PLUS, ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.55 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.75 Details: 25% PEG8000, 0.1M SODIUM ACETATE, 0.1M HEPES-NAOH, pH 7.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2010 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.25→56.63 Å / Num. all: 40016 / Num. obs: 39856 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.64 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.22 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 3.69 % / Mean I/σ(I) obs: 4.7 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1BOU Resolution: 2.25→56.63 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.373 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.231 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→56.63 Å
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Refine LS restraints |
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