+Open data
-Basic information
Entry | Database: PDB / ID: 4yg4 | ||||||
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Title | HipB-O1-O1* complex | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / persistence / multidrug resistance / transcription / higher-order complex / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information toxin-antitoxin complex / regulation of growth / DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MAD / molecular replacement / Resolution: 3.5 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Citation | Journal: Nature / Year: 2015 Title: HipBA-promoter structures reveal the basis of heritable multidrug tolerance. Authors: Schumacher, M.A. / Balani, P. / Min, J. / Chinnam, N.B. / Hansen, S. / Vulic, M. / Lewis, K. / Brennan, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yg4.cif.gz | 94.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yg4.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yg4_validation.pdf.gz | 466.9 KB | Display | wwPDB validaton report |
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Full document | 4yg4_full_validation.pdf.gz | 491.2 KB | Display | |
Data in XML | 4yg4_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 4yg4_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/4yg4 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/4yg4 | HTTPS FTP |
-Related structure data
Related structure data | 4yg1C 4yg7C 5k98C 3dnvS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 8060.239 Da / Num. of mol.: 4 / Fragment: UNP residues 4-74 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: hipB, b1508, JW1501 / Production host: Escherichia coli (E. coli) / References: UniProt: P23873 #2: DNA chain | | Mass: 8593.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) #3: DNA chain | | Mass: 6142.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 27% PEG8000, 0.1 M MES, pH 6.5 / PH range: 6-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→78.3 Å / Num. all: 6970 / Num. obs: 6721 / % possible obs: 96 % / Redundancy: 1.8 % / Net I/σ(I): 7.5 |
Reflection shell | Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 1.5 |
-Phasing
Phasing |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DNV Resolution: 3.5→78.3 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 119.879 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 241.67 Å2 / Biso mean: 163.0347 Å2 / Biso min: 83.61 Å2
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Refinement step | Cycle: final / Resolution: 3.5→78.3 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 3.5 Å / Rfactor Rwork: 0.38 | ||||||||||||||||||||||||||||
Xplor file |
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