+Open data
-Basic information
Entry | Database: PDB / ID: 1yvd | ||||||
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Title | GppNHp-Bound Rab22 GTPase | ||||||
Components | Ras-related protein Rab-22A | ||||||
Keywords | PROTEIN TRANSPORT / Rab GTPase / Rab22 / Vesicular trafficking | ||||||
Function / homology | Function and homology information RAB geranylgeranylation / regulation of vesicle size / endosome organization / endomembrane system / phagocytic vesicle / ruffle / intracellular protein transport / endocytosis / phagocytic vesicle membrane / GDP binding ...RAB geranylgeranylation / regulation of vesicle size / endosome organization / endomembrane system / phagocytic vesicle / ruffle / intracellular protein transport / endocytosis / phagocytic vesicle membrane / GDP binding / actin cytoskeleton / late endosome / endosome membrane / early endosome / GTPase activity / GTP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structural basis of family-wide Rab GTPase recognition by rabenosyn-5. Authors: Eathiraj, S. / Pan, X. / Ritacco, C. / Lambright, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yvd.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yvd.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 1yvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yvd_validation.pdf.gz | 751.4 KB | Display | wwPDB validaton report |
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Full document | 1yvd_full_validation.pdf.gz | 752.9 KB | Display | |
Data in XML | 1yvd_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 1yvd_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/1yvd ftp://data.pdbj.org/pub/pdb/validation_reports/yv/1yvd | HTTPS FTP |
-Related structure data
Related structure data | 1yu9C 1yzkC 1yzlC 1yzmC 1yznC 1yzqC 1yztC 1yzuC 1z06C 1z07C 1z08C 1z0aC 1z0dC 1z0fC 1z0iC 1z0jC 1z0kC 1z22C 1z2aC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19094.717 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab22a, Rab22 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL cells / References: UniProt: P35285 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GNP / |
#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: 2.07 Å3/Da / Density % sol: 40.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG6000, Lithium chloride, MES, Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2003 |
Radiation | Monochromator: confocal blue optic device / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.905→50 Å / Num. obs: 13168 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 31 Å2 / Rsym value: 0.086 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 9 % / Mean I/σ(I) obs: 10.4 / Num. unique all: 1050 / Rsym value: 0.224 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Rab3a polyalanine Resolution: 1.93→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.735 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.098 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.975 Å / Total num. of bins used: 20
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