+Open data
-Basic information
Entry | Database: PDB / ID: 4ob4 | ||||||
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Title | Structure of the S. venezulae BldD DNA-binding domain | ||||||
Components | Putative DNA-binding protein | ||||||
Keywords | DNA BINDING PROTEIN / BldD DNA binding domain / helix turn helix | ||||||
Function / homology | Function and homology information DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / nucleotide binding Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor A3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | schumacher, M.A. / Tschowri, N. / Buttner, M. / Brennan, R. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2014 Title: Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development. Authors: Tschowri, N. / Schumacher, M.A. / Schlimpert, S. / Chinnam, N.B. / Findlay, K.C. / Brennan, R.G. / Buttner, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ob4.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ob4.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ob4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ob4_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 4ob4_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 4ob4_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 4ob4_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/4ob4 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4ob4 | HTTPS FTP |
-Related structure data
Related structure data | 4oayC 4oazC 5khdC 2ewtS 4oax S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 7883.973 Da / Num. of mol.: 3 / Fragment: DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NCIMB 12804 / NRRL 8165 / MA-4680 Gene: bldD, SAV_6861, SCO1489 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7AKQ8 #2: Water | ChemComp-HOH / | |
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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: 2.29 Å3/Da / Density % sol: 46.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG 400, 0.1 M MgCl2, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: Mar 12, 2013 / Details: mirrors |
Radiation | Monochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→69.256 Å / Num. obs: 5897 / % possible obs: 99.9 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 12.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2EWT Resolution: 2.8→69.256 Å / SU ML: 0.45 / σ(F): 1.38 / Phase error: 28.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.906 Å2 / ksol: 0.376 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→69.256 Å
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Refine LS restraints |
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LS refinement shell |
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