+Open data
-Basic information
Entry | Database: PDB / ID: 4oaz | ||||||
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Title | BldD CTD-c-di-GMP complex | ||||||
Components | Putative DNA-binding protein | ||||||
Keywords | DNA BINDING PROTEIN / BldD / c-di-GMP / dimerizer | ||||||
Function / homology | Function and homology information DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / nucleotide binding / negative regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Schumacher, M.A. / Tschowri, N. / Buttner, M. / Brennan, R.G. | ||||||
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 | 4oaz.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oaz.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 4oaz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/4oaz ftp://data.pdbj.org/pub/pdb/validation_reports/oa/4oaz | HTTPS FTP |
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-Related structure data
Related structure data | 4oayC 4ob4C 5khdC 4oax C: citing same article (ref.) |
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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: 10135.400 Da / Num. of mol.: 2 / Fragment: bldd cdomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO1489 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7AKQ8 #2: Chemical | ChemComp-C2E / #3: 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: 2.17 Å3/Da / Density % sol: 43.44 % |
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Crystal grow | Temperature: 298 K / pH: 6.5 Details: sodium/potassium phosphate, pH 6.5, 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 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→34.6 Å / Num. obs: 8186 / % possible obs: 94 % / Observed criterion σ(I): 0 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→34.56 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 32.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.15 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.25→34.56 Å
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Refine LS restraints |
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LS refinement shell |
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