[English] 日本語
Yorodumi- PDB-5yyu: Crystal structure of Staphylococcus aureus single-stranded DNA-bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yyu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Staphylococcus aureus single-stranded DNA-binding protein SsbB | ||||||
Components | Single-stranded DNA-binding protein | ||||||
Keywords | DNA BINDING PROTEIN / single-strand DNA binding protein / Staphylococcus aureus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus ED98 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.984 Å | ||||||
Authors | Huang, Y.H. / Huang, C.Y. | ||||||
Citation | Journal: Rsc Adv / Year: 2018 Title: Characterization of single-stranded DNA-binding protein SsbB from Staphylococcus aureus: SsbB cannot stimulate PriA helicase. Authors: Chen, K.L. / Cheng, J.H. / Lin, C.Y. / Huang, Y.H. / Huang, C.Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yyu.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yyu.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 5yyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yyu_validation.pdf.gz | 456.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5yyu_full_validation.pdf.gz | 466.4 KB | Display | |
Data in XML | 5yyu_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 5yyu_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/5yyu ftp://data.pdbj.org/pub/pdb/validation_reports/yy/5yyu | HTTPS FTP |
-Related structure data
Related structure data | 5xgtS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12659.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus ED98 (bacteria) Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A3F2YLU4*PLUS #2: Water | ChemComp-HOH / | Sequence details | NCBI Reference Sequence: WP_000934795.1 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 100mM Tris pH 8.5, 200mM Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→30 Å / Num. obs: 9841 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.98→3.09 Å / Mean I/σ(I) obs: 2.54 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XGT Resolution: 2.984→29.981 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.35 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.984→29.981 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|