+Open data
-Basic information
Entry | Database: PDB / ID: 8kb9 | ||||||
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Title | Structure of the WDR91 WD40 domain | ||||||
Components | WD repeat-containing protein 91 | ||||||
Keywords | ENDOCYTOSIS / Effector / GTPase / WD40 | ||||||
Function / homology | Function and homology information phosphatidylinositol 3-kinase inhibitor activity / phosphatidylinositol 3-kinase regulator activity / early endosome to late endosome transport / regulation of protein catabolic process / CDC42 GTPase cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / late endosome membrane / early endosome membrane / endosome membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Li, J. / Ma, X.L. / Banerjee, S. / Dong, Z.G. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of the WDR91 WD40 domain Authors: Li, J. / Ma, X.L. / Banerjee, S. / Dong, Z.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kb9.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kb9.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 8kb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kb9_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 8kb9_full_validation.pdf.gz | 432.3 KB | Display | |
Data in XML | 8kb9_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 8kb9_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/8kb9 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/8kb9 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39824.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR91 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A4D1P6 |
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#2: Water | ChemComp-HOH / |
-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: 44.69 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M ammonium citrate tribasic pH 7.0, 8% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.33 Å / Num. obs: 28408 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 40.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 1.081 / Num. unique obs: 1807 / CC1/2: 0.794 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.33 Å / SU ML: 0.2009 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1253 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: 48.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→47.33 Å
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Refine LS restraints |
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LS refinement shell |
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