+Open data
-Basic information
Entry | Database: PDB / ID: 6kco | |||||||||
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Title | Shuguo PWWP in complex with ssDNA | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Shuguo / PWWP / histone reader / DNA binding / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information Formation of WDR5-containing histone-modifying complexes / chromatin remodeling / nucleus Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Liu, Y.C. / Huang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Shuguo PWWP in complex with ssDNA Authors: Liu, Y.C. / Huang, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kco.cif.gz | 362.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kco.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6kco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kco_validation.pdf.gz | 579.9 KB | Display | wwPDB validaton report |
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Full document | 6kco_full_validation.pdf.gz | 589 KB | Display | |
Data in XML | 6kco_validation.xml.gz | 47.8 KB | Display | |
Data in CIF | 6kco_validation.cif.gz | 71.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/6kco ftp://data.pdbj.org/pub/pdb/validation_reports/kc/6kco | HTTPS FTP |
-Related structure data
Related structure data | 6kcpC 6kd6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 9658.010 Da / Num. of mol.: 16 / Fragment: PWWP domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dmel\CG7946, CG7946, Dmel_CG7946 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VAA9 #2: DNA chain | Mass: 1430.974 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 2.13 Å3/Da / Density % sol: 42.2 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl, pH 8.5and 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 55088 / % possible obs: 96.26 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.05 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.234 / Num. unique obs: 5126 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KD6 Resolution: 2.4→29.94 Å / SU ML: 0.2702 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.2361 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.94 Å
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Refine LS restraints |
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LS refinement shell |
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