+Open data
-Basic information
Entry | Database: PDB / ID: 3wr9 | ||||||
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Title | Crystal structure of the Anaerobic DesB-Gallate complex | ||||||
Components | Gallate dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / EXTRADIOL DIOXYGENASE / FE2+ BINDING / DOMAIN-SWAP DIMER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sphingomonas paucimobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sugimoto, K. / Senda, M. / Kasai, D. / Fukuda, M. / Masai, E. / Senda, T. | ||||||
Citation | Journal: Plos One / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wr9.cif.gz | 173.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wr9.ent.gz | 139 KB | Display | PDB format |
PDBx/mmJSON format | 3wr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wr9_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 3wr9_full_validation.pdf.gz | 449.1 KB | Display | |
Data in XML | 3wr9_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 3wr9_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/3wr9 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/3wr9 | HTTPS FTP |
-Related structure data
Related structure data | 3wkuC 3wpmC 3wr3C 3wr4C 3wr8C 3wraC 3wrbC 3wrcC C: citing same article (ref.) |
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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: 46953.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: SYK-6 / Gene: desB / Plasmid: PEVK3G / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q5NTE5, UniProt: G2IKE5*PLUS, linoleate 9S-lipoxygenase #2: Chemical | ChemComp-FE2 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.03 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 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: 2.4→53.2 Å / Num. all: 40594 / Num. obs: 40553 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.77 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 16.58 |
Reflection shell | Resolution: 2.4→2.52 Å / Redundancy: 9.02 % / Mean I/σ(I) obs: 4.28 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DesB substrate-free form Resolution: 2.4→53.17 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.046 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.245 / 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: 28.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→53.17 Å
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Refine LS restraints |
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