+Open data
-Basic information
Entry | Database: PDB / ID: 3law | ||||||
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Title | Structure of GTP-bound L129F mutant Rab7 | ||||||
Components | Ras-related protein Rab-7a | ||||||
Keywords | PROTON TRANSPORT / Protein - Nucleotide complex / Protein Mutant / Charcot-Marie-Tooth disease / Cytoplasmic vesicle / Disease mutation / Endosome / GTP-binding / Lipoprotein / Lysosome / Methylation / Neuropathy / Nucleotide-binding / Phosphoprotein / Prenylation / Protein transport | ||||||
Function / homology | Function and homology information lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / epidermal growth factor catabolic process / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy ...lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / epidermal growth factor catabolic process / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy / establishment of vesicle localization / phagosome maturation / retromer complex binding / endosome to plasma membrane protein transport / protein targeting to lysosome / RAB geranylgeranylation / phagophore assembly site membrane / early endosome to late endosome transport / melanosome membrane / positive regulation of exosomal secretion / intracellular transport / RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / RHOD GTPase cycle / TBC/RABGAPs / retrograde transport, endosome to Golgi / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / viral release from host cell / autophagosome membrane / CDC42 GTPase cycle / RHOH GTPase cycle / autophagosome assembly / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / bone resorption / phagocytic vesicle / lipid catabolic process / Prevention of phagosomal-lysosomal fusion / MHC class II antigen presentation / RAC1 GTPase cycle / lipid droplet / small monomeric GTPase / secretory granule membrane / G protein activity / mitochondrial membrane / response to bacterium / small GTPase binding / synaptic vesicle membrane / endocytosis / positive regulation of protein catabolic process / phagocytic vesicle membrane / GDP binding / late endosome / protein transport / late endosome membrane / lysosome / endosome membrane / lysosomal membrane / GTPase activity / Neutrophil degranulation / GTP binding / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | McCray, B.A. / Skordalakes, E. / Taylor, J.P. | ||||||
Citation | Journal: Hum.Mol.Genet. / Year: 2010 Title: Disease mutations in Rab7 result in unregulated nucleotide exchange and inappropriate activation. Authors: McCray, B.A. / Skordalakes, E. / Taylor, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3law.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3law.ent.gz | 151.9 KB | Display | PDB format |
PDBx/mmJSON format | 3law.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3law_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3law_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3law_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 3law_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/3law ftp://data.pdbj.org/pub/pdb/validation_reports/la/3law | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 23550.734 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB7A, RAB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P51149 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GNP / #4: 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: 2.27 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.2 M sodium formate, 10mM trimethylamine hydrochloride, and 20% polyethylene glycol 3,350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 24170 / Num. obs: 23869 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 0.1 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.8→2.871 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.417 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.88 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.838 / SU B: 35.857 / SU ML: 0.364 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.888 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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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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