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Open data
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Basic information
Entry | Database: PDB / ID: 8cyf | |||||||||
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Title | WhiB3 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA | |||||||||
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![]() | TRANSCRIPTION/DNA/Transferase / redox sensor / transcriptional factor / protein-DNA complex / TRANSCRIPTION / TRANSCRIPTION-DNA-Transferase complex | |||||||||
Function / homology | ![]() response to host redox environment / Actinobacterium-type cell wall biogenesis / 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 ...response to host redox environment / Actinobacterium-type cell wall biogenesis / 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 / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wan, T. / Zhang, L.M. | |||||||||
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 | ![]() | 134.6 KB | Display | ![]() |
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PDB format | ![]() | 89.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8cwrSC ![]() 8cwtC C: citing same article ( S: Starting model for refinement |
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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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 11630.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Full WhiB3 sequence was used for crystallization, the N- and C- terminal residues are not visible due to flexibility. 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 last 82 residues in the C-terminal of the primary sigma factor was fused with the flap tip helix (T815-A829) from RNA polymerase beta subunit, with six histidine tag in the N- ...Details: The last 82 residues in the C-terminal of the primary sigma factor was fused with the flap tip helix (T815-A829) from RNA polymerase beta subunit, with six histidine tag in the N-terminal,The last 82 residues in the C-terminal of the primary sigma factor was fused with the flap tip helix (T815-A829) from RNA polymerase beta subunit, with six histidine tag in the N-terminal Source: (gene. exp.) ![]() ![]() Gene: sigA, ERS007670_01286, ERS007681_03833, ERS007688_01862 Production host: ![]() ![]() References: UniProt: A0A654TMB9, UniProt: A1KGE7, DNA-directed RNA polymerase |
-DNA chain , 2 types, 2 molecules CD
#3: DNA chain | Mass: 4993.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA sequence from WhiB7 promoter / Source: (synth.) ![]() ![]() |
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#4: DNA chain | Mass: 4802.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA sequence from WhiB7 promoter / Source: (synth.) ![]() ![]() |
-Non-polymers , 3 types, 5 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SF4 / |
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#6: Chemical | ChemComp-CAC / |
#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: 2.59 Å3/Da / Density % sol: 52.6 % / Description: Large diamond-shaped crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Ca(Ac)2, 0.1 M Na Cacodylate, pH 6.5, 10%~13% PEG8000 Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: Collected under liquid nitrogen stream Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→50 Å / Num. obs: 13547 / % possible obs: 99.4 % / Redundancy: 15.3 % / Biso Wilson estimate: 66.33 Å2 / CC1/2: 0.987 / CC star: 0.994 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.034 / Rrim(I) all: 0.132 / Χ2: 0.886 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.44→2.49 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.344 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 617 / CC1/2: 0.713 / CC star: 0.912 / Rpim(I) all: 1.441 / Rrim(I) all: 0.508 / Χ2: 0.469 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8CWR Resolution: 2.44→38.15 Å / SU ML: 0.3954 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0463 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→38.15 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 | Refine-ID: X-RAY DIFFRACTION
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