+Open data
-Basic information
Entry | Database: PDB / ID: 8bux | |||||||||
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Title | Rab-binding domain of human MiniBAR | |||||||||
Components | Granule associated Rac and RHOG effector protein 1 | |||||||||
Keywords | PROTEIN TRANSPORT / Rac effector / Rab effector | |||||||||
Function / homology | Function and homology information CCR4-NOT complex binding / Rac protein signal transduction / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / P-body / small GTPase binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å | |||||||||
Authors | Pylypenko, O. / Hammich, H. / Houdusse, A. | |||||||||
Funding support | France, 2items
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Citation | Journal: To Be Published Title: MiniBAR/KIAA0355 is a dual Rac and Rab effector that controls actin contractility and trafficking for successful ciliogenesis Authors: Shaughnessy, R. / Serres, M. / Escot, S. / Hammich, H. / Cuvelier, F. / Rocancourt, M. / Verdon, Q. / Gaffuri, A. / Sourigues, Y. / Malherbe, G. / Velikovsky, L. / Chardon, F. / Thinevez, J. ...Authors: Shaughnessy, R. / Serres, M. / Escot, S. / Hammich, H. / Cuvelier, F. / Rocancourt, M. / Verdon, Q. / Gaffuri, A. / Sourigues, Y. / Malherbe, G. / Velikovsky, L. / Chardon, F. / Thinevez, J. / Callebaut, I. / Formstecher, E. / Houdusse, A. / David, N. / Pylypenko, O. / Echard, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bux.cif.gz | 213.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bux.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 8bux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bux_validation.pdf.gz | 446.2 KB | Display | wwPDB validaton report |
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Full document | 8bux_full_validation.pdf.gz | 446.9 KB | Display | |
Data in XML | 8bux_validation.xml.gz | 15 KB | Display | |
Data in CIF | 8bux_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/8bux ftp://data.pdbj.org/pub/pdb/validation_reports/bu/8bux | HTTPS FTP |
-Related structure data
Related structure data | 8buyC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 36600.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GARRE1, KIAA0355 / Production host: Escherichia coli (E. coli) / References: UniProt: O15063 | ||||||
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#2: Chemical | ChemComp-EDO / | ||||||
#3: Chemical | #4: Chemical | ChemComp-MG / | #5: 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: 1.95 Å3/Da / Density % sol: 36.81 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 1.856→28.58 Å / Num. obs: 24856 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.06 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.856→1.888 Å / Num. unique obs: 4668 / CC1/2: 0.849 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.86→28.58 Å / SU ML: 0.1573 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.8547 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: 34.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→28.58 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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