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- PDB-8cwr: Complex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip ch... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cwr | |||||||||
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Title | Complex structure of WhiB3 and the SigmaAr4-RNAP Beta flap tip chimera in space group R3 | |||||||||
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![]() | TRANSCRIPTION / redox sensor / transcriptional factor | |||||||||
Function / homology | ![]() response to host redox environment / Actinobacterium-type cell wall biogenesis / response to water / Antimicrobial action and antimicrobial resistance in Mtb / dinitrosyl-iron complex binding / protein-disulfide reductase (NAD(P)H) activity / iron-sulfur cluster binding / sigma factor activity / regulation of lipid metabolic process / protein-disulfide reductase activity ...response to host redox environment / Actinobacterium-type cell wall biogenesis / response to water / Antimicrobial action and antimicrobial resistance in Mtb / dinitrosyl-iron complex binding / protein-disulfide reductase (NAD(P)H) activity / iron-sulfur cluster binding / sigma factor activity / regulation of lipid metabolic process / protein-disulfide reductase activity / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / cell redox homeostasis / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 4 iron, 4 sulfur cluster binding / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wan, T. / Zhang, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis. Authors: Wan, T. / Horova, M. / Khetrapal, V. / Li, S. / Jones, C. / Schacht, A. / Sun, X. / Zhang, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110 KB | Display | ![]() |
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PDB format | ![]() | 73.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cwtSC ![]() 8cyfC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 10268.640 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first five residues are not observed in the final structure Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 12650.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The 82 residues in the C-terminal of RNA polymerase sigma factor was fused with the flap tip helix (T815-A829) from RNA polymerase beta subunit, with six histidine tag at the N-terminus Source: (gene. exp.) ![]() ![]() Gene: sigA, mysA, rpoD, rpoV, Rv2703, MTCY05A6.24, rpoB, Rv0667, MTCI376.08c Production host: ![]() ![]() References: UniProt: P9WGI1, UniProt: P9WGY9, DNA-directed RNA polymerase |
-Non-polymers , 5 types, 112 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SF4 / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.4 % / Description: Tiny triangle-shaped crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 10-20 mM NiCl2, 0.8-1.0 M Li2SO4 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Collect under Liquid Nitrogen stream / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 27421 / % possible obs: 99.8 % / Redundancy: 18.1 % / Biso Wilson estimate: 26.01 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.018 / Rrim(I) all: 0.079 / Χ2: 1.092 / Net I/σ(I): 45.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 14.2 % / Rmerge(I) obs: 2.16 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2696 / CC1/2: 0.713 / CC star: 0.922 / Rpim(I) all: 0.578 / Rrim(I) all: 2.239 / Χ2: 0.575 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8CWT Resolution: 1.5→34.87 Å / SU ML: 0.2003 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.139 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: Refined with Phenix.refine GUI. Both B-factors and individual B-factors are refined.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→34.87 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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