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- PDB-2o8x: Crystal structure of the "-35 element" promoter recognition domai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2o8x | ||||||
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Title | Crystal structure of the "-35 element" promoter recognition domain of Mycobacterium tuberculosis SigC | ||||||
![]() | Probable RNA polymerase sigma-C factor | ||||||
![]() | TRANSCRIPTION / promoter recognition / transcription regulation / helix-turn-helix motif | ||||||
Function / homology | ![]() response to water / sigma factor activity / DNA-templated transcription initiation / response to heat / response to hypoxia / response to xenobiotic stimulus / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thakur, K.G. / Joshi, A.M. / Gopal, B. | ||||||
![]() | ![]() Title: Structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function sigma factor sigma(C) from Mycobacterium tuberculosis. Authors: Thakur, K.G. / Joshi, A.M. / Gopal, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48 KB | Display | ![]() |
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PDB format | ![]() | 36 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.7 KB | Display | ![]() |
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Full document | ![]() | 474.4 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2o7gC ![]() 1or7S C: citing same article ( S: Starting model for refinement |
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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: 7386.354 Da / Num. of mol.: 3 / Fragment: Region 4, Promoter -35 element recognition domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8M ammonium sulphate, 0.1M MES (pH 6.5), 1mM DTT, 5% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 6, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→40.29 Å / Num. obs: 7040 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Redundancy: 3.4 % / Rsym value: 0.105 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 1002 / Rsym value: 0.546 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OR7 Resolution: 3→37.01 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.841 / SU B: 16.305 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R: 0.744 / ESU R Free: 0.38 / 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: 47.157 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→37.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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