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Yorodumi- PDB-4u88: Structure of the DNA-Binding Domain of the Response Regulator Sae... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u88 | ||||||
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Title | Structure of the DNA-Binding Domain of the Response Regulator SaeR from Staphylococcus aureus | ||||||
Components | Transcriptional regulator SaeR | ||||||
Keywords | DNA BINDING PROTEIN / DNA-binding protein / transcriptional | ||||||
Function / homology | Function and homology information phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus USA300-ISMMS1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.355 Å | ||||||
Authors | Liu, J.S. / Huang, C.H. / Yang, C.S. / Chen, S.C. / Chen, Y. | ||||||
Citation | Journal: To Be Published Title: Structure of the DNA-Binding Domain of the Response Regulator SaeR from Staphylococcus aureus Authors: Liu, J.S. / Huang, C.H. / Yang, C.S. / Chen, S.C. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u88.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u88.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 4u88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/4u88 ftp://data.pdbj.org/pub/pdb/validation_reports/u8/4u88 | HTTPS FTP |
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-Related structure data
Related structure data | 4ixaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13161.806 Da / Num. of mol.: 2 / Fragment: UNP residues 128-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus USA300-ISMMS1 (bacteria) Gene: AZ30_03680 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: W6DZ35, UniProt: A0A0M3KKX4*PLUS #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: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 5% v/v Tacsimate, pH 7.0, 0.1M HEPES pH 7.0, 10% w/v Polyethylene glycol monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→30 Å / Num. obs: 9992 / % possible obs: 99.6 % / Redundancy: 9.4 % / Net I/σ(I): 19.7 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IXA Resolution: 2.355→29.521 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.355→29.521 Å
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Refine LS restraints |
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LS refinement shell |
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