+Open data
-Basic information
Entry | Database: PDB / ID: 1yzt | ||||||
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Title | GppNHp-Bound Rab21 GTPase at 2.05 A Resolution | ||||||
Components | Ras-related protein Rab-21 | ||||||
Keywords | PROTEIN TRANSPORT / Rab GTPase / Rab21 / Vesicular Trafficking | ||||||
Function / homology | Function and homology information cytoplasmic side of early endosome membrane / Rab protein signal transduction / positive regulation of early endosome to late endosome transport / RAB geranylgeranylation / regulation of exocytosis / RAB GEFs exchange GTP for GDP on RABs / vesicle membrane / anterograde axonal transport / regulation of axon extension / positive regulation of dendrite morphogenesis ...cytoplasmic side of early endosome membrane / Rab protein signal transduction / positive regulation of early endosome to late endosome transport / RAB geranylgeranylation / regulation of exocytosis / RAB GEFs exchange GTP for GDP on RABs / vesicle membrane / anterograde axonal transport / regulation of axon extension / positive regulation of dendrite morphogenesis / Golgi cisterna membrane / cleavage furrow / endomembrane system / axon cytoplasm / intracellular protein transport / trans-Golgi network / cytoplasmic side of plasma membrane / positive regulation of receptor-mediated endocytosis / GDP binding / early endosome membrane / protein stabilization / early endosome / endosome / Golgi membrane / focal adhesion / GTPase activity / synapse / GTP binding / endoplasmic reticulum membrane / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 1yzt.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yzt.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 1yzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yzt ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yzt | HTTPS FTP |
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-Related structure data
Related structure data | 1yu9C 1yvdC 1yzkC 1yzlC 1yzmC 1yznC 1yzqC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20963.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB21, KIAA0118 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL Cells / References: UniProt: Q9UL25 #2: Chemical | #3: Chemical | #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: 2.75 Å3/Da / Density % sol: 54.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18% PEG 6000, 200mM Lithium sufate, 50mM Tris, pH 8.0, 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: Apr 14, 2004 / Details: Osmic mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 23946 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 1952 / Rsym value: 0.368 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Polyalanine Rab3a GTPase Resolution: 2.05→12 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.873 / SU B: 6.231 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.228 / ESU R Free: 0.215 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.139 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.102 Å / Total num. of bins used: 20
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