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Yorodumi- PDB-4lbp: 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG) from Burk... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lbp | ||||||
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Title | 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG) from Burkholderia phenoliruptrix AC1100: Complex with 2,5-dihydroxybenzoquinone | ||||||
Components | 5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG) | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information : / YCII-related / YCII-related domain / Dimeric alpha+beta barrel / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Burkholderia cepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Hayes, R.P. / Lewis, K.M. / Xun, L. / Kang, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Catalytic Mechanism of 5-Chlorohydroxyhydroquinone Dehydrochlorinase from the YCII Superfamily of Largely Unknown Function. Authors: Hayes, R.P. / Lewis, K.M. / Xun, L. / Kang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lbp.cif.gz | 30.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lbp.ent.gz | 23.5 KB | Display | PDB format |
PDBx/mmJSON format | 4lbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/4lbp ftp://data.pdbj.org/pub/pdb/validation_reports/lb/4lbp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11322.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cepacia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q45075 |
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#2: Chemical | ChemComp-1WG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.41 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% (w/v) polyethylene glycol 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2012 | |||||||||||||||||||||
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.87→50 Å / Num. all: 10578 / Num. obs: 10578 / % possible obs: 99.9 % / Observed criterion σ(I): -3 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→45.096 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.94 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→45.096 Å
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Refine LS restraints |
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LS refinement shell |
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