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Yorodumi- PDB-8k70: Structural basis for the distinct roles of non-conserved Pro116 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k70 | |||||||||
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Title | Structural basis for the distinct roles of non-conserved Pro116 and conserved Tyr124 of BCH domain of yeast p50RhoGAP | |||||||||
Components | Putative Rho GTPase-activating protein C1565.02c | |||||||||
Keywords | LIPID BINDING PROTEIN / GTPase-activating protein / Rho / Scaffold | |||||||||
Function / homology | Function and homology information : / phospholipid transfer activity / intermembrane phospholipid transfer / GTPase activator activity / Golgi apparatus / signal transduction Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe 972h- (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | |||||||||
Authors | Shankar, S. / Sivaraman, J. | |||||||||
Funding support | Singapore, 2items
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Citation | Journal: Cell.Mol.Life Sci. / Year: 2024 Title: Structural basis for the distinct roles of non-conserved Pro116 and conserved Tyr124 of BCH domain of yeast p50RhoGAP. Authors: Shankar, S. / Chew, T.W. / Chichili, V.P.R. / Low, B.C. / Sivaraman, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k70.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k70.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 8k70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k70_validation.pdf.gz | 468.5 KB | Display | wwPDB validaton report |
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Full document | 8k70_full_validation.pdf.gz | 488 KB | Display | |
Data in XML | 8k70_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 8k70_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/8k70 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/8k70 | 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: 17907.658 Da / Num. of mol.: 4 / Mutation: P116A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast) Strain: 972 / Gene: SPAC1565.02c Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9P3B1 #2: Chemical | ChemComp-PG4 / Has ligand of interest | N | |
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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: 5.88 Å3/Da / Density % sol: 79.08 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris propane pH 7.0 and 2.1 M NaCl |
-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: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.64 Å / Num. obs: 37961 / % possible obs: 93.83 % / Redundancy: 5 % / Biso Wilson estimate: 79.17 Å2 / Rsym value: 0.14 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.8→2.87 Å / Rmerge(I) obs: 0.23 / Num. unique obs: 2084 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→46.81 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 30.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→46.81 Å
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Refine LS restraints |
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LS refinement shell |
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