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- PDB-2y79: STRUCTURE OF THE FIRST GAF DOMAIN E87A MUTANT OF MYCOBACTERIUM TU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y79 | ||||||
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Title | STRUCTURE OF THE FIRST GAF DOMAIN E87A MUTANT OF MYCOBACTERIUM TUBERCULOSIS DOSS | ||||||
![]() | REDOX SENSOR HISTIDINE KINASE RESPONSE REGULATOR DEVS | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cho, H.Y. / Cho, H.J. / Kang, B.S. | ||||||
![]() | ![]() Title: Blockage of the Channel to Heme by the E87 Side Chain in the Gaf Domain of Mycobacterium Tuberculosis Doss Confers the Unique Sensitivity of Doss to Oxygen. Authors: Cho, H.Y. / Cho, H.J. / Kim, M.H. / Kang, B.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.5 KB | Display | ![]() |
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PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y8hC ![]() 2w3dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16697.957 Da / Num. of mol.: 2 / Fragment: RESIDUES 63-210 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P95194, UniProt: P9WGK3*PLUS, histidine kinase #2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 7 Details: 19% PEG 6000, 200 MM CALCIUM ACETATE, 100 MM TRIS PH 7.0. |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2399 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 29661 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.8→31.4 Å / Redundancy: 6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.3 / % possible all: 86.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W3D Resolution: 1.8→31.39 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.866 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.139 / 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: 23.518 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→31.39 Å
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Refine LS restraints |
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