+Open data
-Basic information
Entry | Database: PDB / ID: 2rkl | ||||||
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Title | Crystal Structure of S.cerevisiae Vta1 C-terminal domain | ||||||
Components | Vacuolar protein sorting-associated protein VTA1Vacuole | ||||||
Keywords | LIPID TRANSPORT / dimerization motif / Cytoplasm / Endosome / Membrane / Protein transport / Transport | ||||||
Function / homology | Function and homology information ESCRT IV complex / late endosome to vacuole transport via multivesicular body sorting pathway / late endosome to vacuole transport / lipid transport / ATPase activator activity / multivesicular body / protein-macromolecule adaptor activity / protein transport / endosome Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Xiao, J. / Xia, H. / Zhou, J. / Xu, Z. | ||||||
Citation | Journal: Dev.Cell / Year: 2008 Title: Structural basis of vta1 function in the multivesicular body sorting pathway. Authors: Xiao, J. / Xia, H. / Zhou, J. / Azmi, I.F. / Davies, B.A. / Katzmann, D.J. / Xu, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rkl.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rkl.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 2rkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/2rkl ftp://data.pdbj.org/pub/pdb/validation_reports/rk/2rkl | 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 5917.778 Da / Num. of mol.: 6 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VTA1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06263 #2: Chemical | ChemComp-MPD / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: MPD, vapor diffusion, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793, 0.9794, 0.9566 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Detector: CCD / Date: Jul 19, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. obs: 59057 / % possible obs: 94.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.062 / Χ2: 1.443 / Net I/σ(I): 16.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.821 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.088 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.774 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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