+Open data
-Basic information
Entry | Database: PDB / ID: 1z2a | ||||||
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Title | GDP-Bound Rab23 GTPase crystallized in P2(1)2(1)2(1) space group | ||||||
Components | Ras-related protein Rab-23 | ||||||
Keywords | PROTEIN TRANSPORT / Rab GTPase / Rab23 / Vesicular trafficking | ||||||
Function / homology | Function and homology information craniofacial suture morphogenesis / RAB geranylgeranylation / spinal cord dorsal/ventral patterning / dorsal/ventral neural tube patterning / regulation of smoothened signaling pathway / GTP metabolic process / embryonic digit morphogenesis / negative regulation of protein import into nucleus / autophagosome assembly / cilium assembly ...craniofacial suture morphogenesis / RAB geranylgeranylation / spinal cord dorsal/ventral patterning / dorsal/ventral neural tube patterning / regulation of smoothened signaling pathway / GTP metabolic process / embryonic digit morphogenesis / negative regulation of protein import into nucleus / autophagosome assembly / cilium assembly / autophagosome / endomembrane system / cellular defense response / phagocytic vesicle / neural tube closure / negative regulation of proteolysis / intracellular protein transport / phagocytic vesicle membrane / cell junction / nervous system development / endosome membrane / GTPase activity / centrosome / GTP binding / signal transduction / proteolysis / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 1z2a.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z2a.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 1z2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/1z2a ftp://data.pdbj.org/pub/pdb/validation_reports/z2/1z2a | HTTPS FTP |
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-Related structure data
Related structure data | 1yu9C 1yvdC 1yzkC 1yzlC 1yzmC 1yznC 1yzqC 1yztC 1yzuC 1z06C 1z07C 1z08C 1z0aC 1z0dC 1z0fC 1z0iC 1z0jC 1z0kC 1z22C 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: 19066.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab23 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: P35288 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GDP / |
#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: 2.14 Å3/Da / Density % sol: 41.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 15% PEG 6000, 50mM Na acetate, pH 5.0, 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: Mar 30, 2004 |
Radiation | Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 12482 / Num. obs: 12522 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 34.8 Å2 / Rsym value: 0.044 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 834 / Rsym value: 0.268 / % possible all: 79.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Polyalanine Rab3a Resolution: 1.9→8 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.189 / 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: 25.353 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.949 Å / Total num. of bins used: 20
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