+Open data
-Basic information
Entry | Database: PDB / ID: 3wrb | ||||||
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Title | Crystal structure of the anaerobic H124F 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: 2.1 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 | 3wrb.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wrb.ent.gz | 143.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/3wrb ftp://data.pdbj.org/pub/pdb/validation_reports/wr/3wrb | HTTPS FTP |
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-Related structure data
Related structure data | 3wkuC 3wpmC 3wr3C 3wr4C 3wr8C 3wr9C 3wraC 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: 46962.191 Da / Num. of mol.: 2 / Mutation: H124F 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 | #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: 2.34 Å3/Da / Density % sol: 47.45 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.97951 / Wavelength: 0.97951 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2010 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→58.5 Å / Num. all: 50950 / Num. obs: 50339 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.17 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.16 % / Mean I/σ(I) obs: 6.94 / % possible all: 98.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DesB substrate-free form Resolution: 2.1→58 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.137 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.199 / 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: 22.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→58 Å
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Refine LS restraints |
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