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- PDB-3wra: Crystal structure of the desB-Gallate complex exposed to Aerobic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wra | ||||||
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Title | Crystal structure of the desB-Gallate complex exposed to Aerobic Atomosphere | ||||||
![]() | Gallate dioxygenase | ||||||
![]() | OXIDOREDUCTASE / EXTRADIOL DIOXYGENASE / FE2+ BINDING / DOMAIN-SWAP DIMER | ||||||
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 | ![]() | 171.1 KB | Display | ![]() |
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PDB format | ![]() | 135.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.2 KB | Display | ![]() |
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Full document | ![]() | 437.1 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wkuC ![]() 3wpmC ![]() 3wr3C ![]() 3wr4C ![]() 3wr8C ![]() 3wr9C ![]() 3wrbC ![]() 3wrcC C: citing same article ( |
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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, linoleate 9S-lipoxygenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.92 % |
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Crystal grow | Temperature: 293 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 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2010 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→56.7 Å / Num. all: 50424 / Num. obs: 49264 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.47 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.52 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.59 % / Mean I/σ(I) obs: 4.71 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: DesB substrate-free form Resolution: 2.1→55 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.148 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.206 / 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: 34.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→55 Å
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Refine LS restraints |
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