+Open data
-Basic information
Entry | Database: PDB / ID: 1z0a | ||||||
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Title | GDP-Bound Rab2A GTPase | ||||||
Components | Ras-related protein Rab-2A | ||||||
Keywords | PROTEIN TRANSPORT / Rab GTPase / Rab2 / Vesicular trafficking | ||||||
Function / homology | Function and homology information RAB geranylgeranylation / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi organization / endoplasmic reticulum to Golgi vesicle-mediated transport / post-translational protein modification / endoplasmic reticulum-Golgi intermediate compartment membrane / GDP binding / melanosome / protein transport / Golgi membrane ...RAB geranylgeranylation / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi organization / endoplasmic reticulum to Golgi vesicle-mediated transport / post-translational protein modification / endoplasmic reticulum-Golgi intermediate compartment membrane / GDP binding / melanosome / protein transport / Golgi membrane / lysosomal membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 | 1z0a.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z0a.ent.gz | 119.5 KB | Display | PDB format |
PDBx/mmJSON format | 1z0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z0a_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1z0a_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1z0a_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 1z0a_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/1z0a ftp://data.pdbj.org/pub/pdb/validation_reports/z0/1z0a | HTTPS FTP |
-Related structure data
Related structure data | 1yu9C 1yvdC 1yzkC 1yzlC 1yzmC 1yznC 1yzqC 1yztC 1yzuC 1z06C 1z07C 1z08C 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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Unit cell |
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-Components
#1: Protein | Mass: 19720.361 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB2, RAB2A / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: P61019 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GDP / #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: 3 Å3/Da / Density % sol: 58.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 15% PEG 4000, 400mM Lithium sulfate, 100mM Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2004 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→50 Å / Num. obs: 49343 / % possible obs: 68.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 45.2 Å2 / Rsym value: 0.069 / Net I/σ(I): 32.9 |
Reflection shell | Resolution: 2.12→2.18 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1880 / Rsym value: 0.377 / % possible all: 45.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Polyalanine Rab4 GTPase Resolution: 2.12→10 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.888 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.208 / ESU R Free: 0.211 / 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: 44.912 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.173 Å / Total num. of bins used: 20
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