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Yorodumi- PDB-6jhe: Crystal Structure of Bacillus subtilis SigW domain 4 in complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jhe | ||||||
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Title | Crystal Structure of Bacillus subtilis SigW domain 4 in complexed with -35 element DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / protein-DNA complex / helix-turn-helix / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information sigma factor activity / DNA-templated transcription initiation / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å | ||||||
Model details | Crystal Structure of Bacillus subtilis SigW domain 4 in complexed with -35 element DNA | ||||||
Authors | Kwon, E. / Devkota, S.R. / Pathak, D. / Dahal, P. / Kim, D.Y. | ||||||
Citation | Journal: Plos One / Year: 2019 Title: Structural analysis of the recognition of the -35 promoter element by SigW from Bacillus subtilis. Authors: Kwon, E. / Devkota, S.R. / Pathak, D. / Dahal, P. / Kim, D.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jhe.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jhe.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jhe_validation.pdf.gz | 437.2 KB | Display | wwPDB validaton report |
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Full document | 6jhe_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 6jhe_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 6jhe_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/6jhe ftp://data.pdbj.org/pub/pdb/validation_reports/jh/6jhe | HTTPS FTP |
-Related structure data
Related structure data | 2h27S S: Starting model for refinement |
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Similar 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: 7380.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: sigW, ybbL, BSU01730 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q45585 |
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#2: DNA chain | Mass: 3323.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 3381.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.68 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 6.5 / Details: PEG 1500, isopropanol, CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 3013 / % possible obs: 99.4 % / Redundancy: 15.1 % / Biso Wilson estimate: 69.04 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 62.8 |
Reflection shell | Resolution: 3→3.18 Å / Rmerge(I) obs: 0.524 / Num. unique obs: 468 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H27 Resolution: 3.101→29.842 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168 Å2 / Biso mean: 69 Å2 / Biso min: 44.16 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.101→29.842 Å
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LS refinement shell | Resolution: 3.101→3.318 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -3.941 Å / Origin y: -20.7209 Å / Origin z: -0.3 Å
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Refinement TLS group | Selection details: all |