+Open data
-Basic information
Entry | Database: PDB / ID: 5d8e | ||||||
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Title | crystal structure of SSB from homo sapiens | ||||||
Components | SOSS complex subunit B1Southern Okanagan Secondary School | ||||||
Keywords | DNA BINDING PROTEIN / single-strand DNA binding | ||||||
Function / homology | Function and homology information SOSS complex / establishment of protein localization to telomere / G-rich strand telomeric DNA binding / mitotic G2/M transition checkpoint / response to ionizing radiation / positive regulation of telomere capping / RNA polymerase II transcribes snRNA genes / DNA polymerase binding / double-strand break repair via homologous recombination / site of double-strand break ...SOSS complex / establishment of protein localization to telomere / G-rich strand telomeric DNA binding / mitotic G2/M transition checkpoint / response to ionizing radiation / positive regulation of telomere capping / RNA polymerase II transcribes snRNA genes / DNA polymerase binding / double-strand break repair via homologous recombination / site of double-strand break / single-stranded DNA binding / chromosome, telomeric region / DNA repair / DNA damage response / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Li, Y.H. / Gao, Z.Q. / Dong, Y.H. | ||||||
Citation | Journal: To Be Published Title: crystal structure of SSB from homo sapiens Authors: Li, Y.H. / Gao, Z.Q. / Dong, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d8e.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d8e.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 5d8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/5d8e ftp://data.pdbj.org/pub/pdb/validation_reports/d8/5d8e | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 13019.521 Da / Num. of mol.: 4 / Fragment: UNP residues 1-109 / Mutation: L70M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NABP2, OBFC2B, SSB1, LP3587 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BQ15 |
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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: 4.45 Å3/Da / Density % sol: 72.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES pH 6.0, 16% Jeffamine M-600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 18515 / Num. obs: 18515 / % possible obs: 98.8 % / Redundancy: 9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 50.1 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 8.65 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→35.914 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.83 / Stereochemistry target values: TWIN_LSQ_F
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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: 3→35.914 Å
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Refine LS restraints |
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LS refinement shell |
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