+Open data
-Basic information
Entry | Database: PDB / ID: 5d8f | ||||||
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Title | crystal structure of SSB and ssDNA complex from homo sapiens | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / single-strand DNA binding / DNA BINDING PROTEIN-DNA complex | ||||||
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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Li, Y.H. / Gao, Z.Q. / Dong, Y.H. | ||||||
Citation | Journal: To Be Published Title: crystal structure of SSB and ssDNA complex 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 | 5d8f.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d8f.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 5d8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d8f_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 5d8f_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 5d8f_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 5d8f_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/5d8f ftp://data.pdbj.org/pub/pdb/validation_reports/d8/5d8f | HTTPS FTP |
-Related structure data
Related structure data | 5d8eS S: Starting model for refinement |
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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: 12860.797 Da / Num. of mol.: 2 / Fragment: UNP residues 1-109 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 #2: DNA chain | | Mass: 2996.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: 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: 2.93 Å3/Da / Density % sol: 57.96 % |
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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: Nov 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 14419 / Num. obs: 14419 / % possible obs: 99.3 % / Redundancy: 19.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 73 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 21.5 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 9.16 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D8E Resolution: 2.35→41.91 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.81 / 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: 2.35→41.91 Å
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Refine LS restraints |
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LS refinement shell |
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