+Open data
-Basic information
Entry | Database: PDB / ID: 6kcu | |||||||||
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Title | Shuguo PWWP domain | |||||||||
Components | LD23804p | |||||||||
Keywords | DNA BINDING PROTEIN / Shuguo / PWWP / histone reader / DNA binding | |||||||||
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) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Liu, Y.C. / Huang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Shuguo PWWP domain 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 | 6kcu.cif.gz | 34.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kcu.ent.gz | 21.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kcu_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
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Full document | 6kcu_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 6kcu_validation.xml.gz | 7 KB | Display | |
Data in CIF | 6kcu_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/6kcu ftp://data.pdbj.org/pub/pdb/validation_reports/kc/6kcu | HTTPS FTP |
-Related structure data
Related structure data | 6kd6C 4fu6S S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9658.010 Da / Num. of mol.: 1 / 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 |
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#2: Chemical | ChemComp-BTB / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.68 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris, pH 5.5, 0.2M NaCl, 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: BL18U1 / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 3, 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: 1.65→30 Å / Num. obs: 10994 / % possible obs: 99.8 % / Redundancy: 16.1 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.476 / Num. unique obs: 1073 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FU6 Resolution: 1.65→29.012 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 20.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→29.012 Å
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Refine LS restraints |
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LS refinement shell |
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