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- PDB-3wpm: Crystal structure of the anaerobic DesB-gallate complex by co-cry... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wpm | ||||||
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Title | Crystal structure of the anaerobic DesB-gallate complex by co-crystallization | ||||||
![]() | Gallate dioxygenase | ||||||
![]() | OXIDOREDUCTASE / type II extradiol dioxygenase / domain-swap dimer / extradiol dioxygenase / Fe2+ binding | ||||||
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 | ![]() | 168.1 KB | Display | ![]() |
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PDB format | ![]() | 131.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451 KB | Display | ![]() |
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Full document | ![]() | 464.5 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wkuSC ![]() 3wr3C ![]() 3wr4C ![]() 3wr8C ![]() 3wr9C ![]() 3wraC ![]() 3wrbC ![]() 3wrcC ![]() 3vju ![]() 3vjv ![]() 3vjw ![]() 3vjx ![]() 3vjy S: Starting model for refinement 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: G2IKE5, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen #2: Chemical | #3: Chemical | ChemComp-GDE / | #4: 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: 47.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.75 Details: 26% 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: May 23, 2012 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→56.3 Å / Num. all: 29276 / Num. obs: 29197 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 40.59 Å2 |
Reflection shell | Resolution: 2.5→2.64 Å / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WKU Resolution: 2.5→43.893 Å / FOM work R set: 0.7063 / SU ML: 0.41 / σ(F): 0.91 / Phase error: 35.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.65 Å2 / Biso mean: 42.19 Å2 / Biso min: 11.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→43.893 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
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