+Open data
-Basic information
Entry | Database: PDB / ID: 2efe | ||||||
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Title | Ara7-GDPNH2/AtVps9a | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / GEF / GTPase / Vps9 / Rab5 / nucleotide | ||||||
Function / homology | Function and homology information cell plate assembly / post-embryonic root development / cell wall biogenesis / intracellular organelle / embryo development ending in seed dormancy / vacuole organization / molecular sequestering activity / multivesicular body membrane / late endosome to vacuole transport / small molecule binding ...cell plate assembly / post-embryonic root development / cell wall biogenesis / intracellular organelle / embryo development ending in seed dormancy / vacuole organization / molecular sequestering activity / multivesicular body membrane / late endosome to vacuole transport / small molecule binding / GTPase activator activity / guanyl-nucleotide exchange factor activity / intracellular protein transport / early endosome membrane / early endosome / endosome / GTPase activity / GTP binding / endoplasmic reticulum / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Ihara, K. / Uejima, T. / Wakatsuki, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system Authors: Uejima, T. / Ihara, K. / Goh, T. / Ito, E. / Sunada, M. / Ueda, T. / Nakano, A. / Wakatsuki, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2efe.cif.gz | 179.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2efe.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 2efe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2efe ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2efe | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30168.316 Da / Num. of mol.: 2 / Fragment: Vps9 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3)pLysS / References: UniProt: Q9LT31 #2: Protein | Mass: 19887.432 Da / Num. of mol.: 2 / Fragment: GTPase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q9SN68 #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: 2.24 Å3/Da / Density % sol: 45.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG3350, 200mM lithium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→100 Å / Num. obs: 49631 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.08→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.4 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: nucleotide-free Ara7/AtVps9a which was solved by MAD Resolution: 2.08→68.52 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.764 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.288 / ESU R Free: 0.231 / 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: 38.447 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→68.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.082→2.136 Å / Total num. of bins used: 20
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