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Yorodumi- PDB-2xva: Crystal structure of the tellurite detoxification protein TehB fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xva | ||||||
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Title | Crystal structure of the tellurite detoxification protein TehB from E. coli in complex with sinefungin | ||||||
Components | TELLURITE RESISTANCE PROTEIN TEHB | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information tellurite methyltransferase / response to tellurium ion / S-adenosylmethionine-dependent methyltransferase activity / methyltransferase activity / response to toxic substance / methylation / response to antibiotic / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Choudhury, H.G. / Cameron, A.D. / Iwata, S. / Beis, K. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Structure and Mechanism of the Chalcogen Detoxifying Protein Tehb from Escherichia Coli. Authors: Choudhury, H.G. / Cameron, A.D. / Iwata, S. / Beis, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xva.cif.gz | 337.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xva.ent.gz | 275.9 KB | Display | PDB format |
PDBx/mmJSON format | 2xva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/2xva ftp://data.pdbj.org/pub/pdb/validation_reports/xv/2xva | HTTPS FTP |
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-Related structure data
Related structure data | 2xvmC 2i6gS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 22674.842 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 MG1655 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25397 #2: Chemical | ChemComp-SFG / #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | SINEFUNGIN IS REPRESENTED AS ADENOSYL-ORNITHINE (SFG). WE OBSERVE SOME POSITIVE DENSITY NEAR THE ...SINEFUNGIN | Sequence details | THE I2V MUTATION WAS FROM CLONING TO THE HO SITE. | |
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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: 2.39 Å3/Da / Density % sol: 48.5 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.2M NAF, 22% PEG 3350, 5MM SINEFUNGIN, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2010 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→42.1 Å / Num. obs: 62310 / % possible obs: 94.6 % / Observed criterion σ(I): 6 / Redundancy: 1.9 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.9 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2I6G Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.621 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.162 / 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: 18.607 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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