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Yorodumi- PDB-2vjw: crystal structure of the second GAF domain of DevS from Mycobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vjw | ||||||
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Title | crystal structure of the second GAF domain of DevS from Mycobacterium smegmatis | ||||||
Components | GAF FAMILY PROTEIN | ||||||
Keywords | HYDROLASE / GAF / HISTIDINE KINASE / HYPOXIA SENSING | ||||||
Function / homology | Function and homology information phosphorelay sensor kinase activity / protein dimerization activity / membrane Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kang, B.S. / Cho, H.Y. / Cho, H.J. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2008 Title: O2- and No-Sensing Mechanism Through the Devsr Two- Component System in Mycobacterium Smegmatis. Authors: Lee, J.M. / Cho, H.Y. / Cho, H.J. / Ko, I.J. / Park, S.W. / Baik, H.S. / Oh, J.H. / Eom, C.Y. / Kim, Y.M. / Kang, B.S. / Oh, J.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vjw.cif.gz | 33.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vjw.ent.gz | 25.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vjw ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vjw | 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
#1: Protein | Mass: 15363.799 Da / Num. of mol.: 1 / Fragment: RESIDUES 232-380 Source method: isolated from a genetically manipulated source Details: 232-373 OF DEVS PROTEIN / Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Plasmid: PGST-PARALLEL1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: A0R2U9 |
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#2: 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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 10102 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.3 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 2→29.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.166 / 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: 33.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.24 Å
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Refine LS restraints |
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