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Yorodumi- PDB-2w3f: Reduced structure of the first GAF domain of Mycobacterium tuberc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w3f | ||||||
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Title | Reduced structure of the first GAF domain of Mycobacterium tuberculosis DosS | ||||||
Components | TWO COMPONENT SENSOR HISTIDINE KINASE DEVS (GAF FAMILY PROTEIN) | ||||||
Keywords | TRANSFERASE / REDOX SENSOR / MYCOBACTERIUM TUBERCULOSIS / HEME / KINASE / HYPOXIA / GAF DOMAIN | ||||||
Function / homology | Function and homology information detection of redox state / carbon monoxide binding / nitric oxide binding / oxygen sensor activity / response to redox state / histidine kinase / phosphorelay sensor kinase activity / peptidoglycan-based cell wall / oxygen binding / protein autophosphorylation ...detection of redox state / carbon monoxide binding / nitric oxide binding / oxygen sensor activity / response to redox state / histidine kinase / phosphorelay sensor kinase activity / peptidoglycan-based cell wall / oxygen binding / protein autophosphorylation / membrane => GO:0016020 / protein dimerization activity / protein kinase activity / heme binding / magnesium ion binding / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kang, B.S. / Cho, H.Y. / Cho, H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural Insight Into the Heme-Based Redox Sensing by Doss from Mycobacterium Tuberculosis. Authors: Cho, H.Y. / Cho, H.J. / Kim, Y.M. / Oh, J.I. / Kang, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w3f.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w3f.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 2w3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/2w3f ftp://data.pdbj.org/pub/pdb/validation_reports/w3/2w3f | 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: 16755.994 Da / Num. of mol.: 2 / Fragment: GAF DOMAIN, RESIDUES 63-210 Source method: isolated from a genetically manipulated source Details: D63 TO K210 OF DOSS WITH ADDITIONAL GAMDP SEQUENCE AT THE N-TERMINUS DUE TO CLONING PROCEDURE Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P95194, UniProt: P9WGK3*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor #2: Chemical | #3: 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: 2.28 Å3/Da / Density % sol: 45.66 % / Description: NONE |
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Crystal grow | Details: 20% PEG4000, 0.2M CALCIUM CHLORIDE IN TRIS-HCL, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 40766 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 12.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 50.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.52 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.778 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.1 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.524 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→34.52 Å
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Refine LS restraints |
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