+Open data
-Basic information
Entry | Database: PDB / ID: 6hh2 | ||||||
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Title | Rab29 small GTPase bound to GDP | ||||||
Components | Ras-related protein Rab-7L1 | ||||||
Keywords | SIGNALING PROTEIN / Rab GTPase / membrane trafficking | ||||||
Function / homology | Function and homology information protein localization to ciliary membrane / : / modulation by host of viral process / regulation of retrograde transport, endosome to Golgi / melanosome organization / RAB geranylgeranylation / positive regulation of intracellular protein transport / cis-Golgi network / protein localization to membrane / vacuole ...protein localization to ciliary membrane / : / modulation by host of viral process / regulation of retrograde transport, endosome to Golgi / melanosome organization / RAB geranylgeranylation / positive regulation of intracellular protein transport / cis-Golgi network / protein localization to membrane / vacuole / retrograde transport, endosome to Golgi / dynein complex binding / positive regulation of receptor recycling / intracellular vesicle / positive regulation of T cell receptor signaling pathway / Golgi organization / kinesin binding / endomembrane system / synapse assembly / mitochondrion organization / T cell activation / response to bacterium / intracellular protein transport / trans-Golgi network / recycling endosome / small GTPase binding / GDP binding / melanosome / negative regulation of neuron projection development / cell differentiation / cytoskeleton / early endosome / intracellular membrane-bounded organelle / GTPase activity / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å | ||||||
Authors | Khan, A.R. / McGrath, E. / Waschbusch, D. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: Small GTPases / Year: 2019 Title: LRRK2 binds to the Rab32 subfamily in a GTP-dependent mannerviaits armadillo domain. Authors: McGrath, E. / Waschbusch, D. / Baker, B.M. / Khan, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hh2.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hh2.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 6hh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/6hh2 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/6hh2 | HTTPS FTP |
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-Related structure data
Related structure data | 6ff8C 6hduSC 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
#1: Protein | Mass: 20487.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB29, RAB7L1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14966 |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
#4: 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: 3.15 Å3/Da / Density % sol: 60.95 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / Details: 2M NaCl 0.1M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.449→86.35 Å / Num. obs: 46405 / % possible obs: 99.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.017 / Rrim(I) all: 0.055 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.449→1.47 Å / Rmerge(I) obs: 1.631 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.68 / Rpim(I) all: 0.585 / Rsym value: 1.736 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6hdu Resolution: 1.449→62.319 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 18.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.449→62.319 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 37.5723 Å / Origin y: 16.2535 Å / Origin z: 32.9528 Å
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Refinement TLS group | Selection details: all |