+Open data
-Basic information
Entry | Database: PDB / ID: 6b3y | ||||||
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Title | Crystal structure of the PH-like domain from DENND3 | ||||||
Components | DENN domain-containing protein 3 | ||||||
Keywords | TRANSPORT PROTEIN / autophagy / guanine nucleotide exchange factor / PH-like fold | ||||||
Function / homology | Function and homology information regulation of Rab protein signal transduction / protein catabolic process => GO:0030163 / RAB GEFs exchange GTP for GDP on RABs / endosome to lysosome transport / guanyl-nucleotide exchange factor activity / cytoplasmic vesicle Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.852 Å | ||||||
Authors | Kozlov, G. / Xu, J. / Menade, M. / Beaugrand, M. / Pan, T. / McPherson, P.S. / Gehring, K. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: A PH-like domain of the Rab12 guanine nucleotide exchange factor DENND3 binds actin and is required for autophagy. Authors: Xu, J. / Kozlov, G. / McPherson, P.S. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b3y.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b3y.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 6b3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/6b3y ftp://data.pdbj.org/pub/pdb/validation_reports/b3/6b3y | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29241.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dennd3, Kiaa0870 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A2RT67 #2: 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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.24 M sodium malonate pH 7.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9768 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 46621 / % possible obs: 97.76 % / Redundancy: 7.8 % / Rsym value: 0.061 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4568 / Rsym value: 0.647 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.852→32.615 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.852→32.615 Å
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Refine LS restraints |
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LS refinement shell |
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