+Open data
-Basic information
Entry | Database: PDB / ID: 1z2x | ||||||
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Title | Crystal structure of mouse Vps29 | ||||||
Components | Vacuolar protein sorting 29Vacuole | ||||||
Keywords | PROTEIN TRANSPORT / Vps29 / retromer / phosphatase | ||||||
Function / homology | Function and homology information WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / Golgi to vacuole transport / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / endosome membrane / endosome / intracellular membrane-bounded organelle ...WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / Golgi to vacuole transport / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / endosome membrane / endosome / intracellular membrane-bounded organelle / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.22 Å | ||||||
Authors | Collins, B.M. / Skinner, C.F. / Watson, P.J. / Seaman, M.N.J. / Owen, D.J. | ||||||
Citation | Journal: NAT.STRUCT.MOL.BIOL. / Year: 2005 Title: Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly Authors: Collins, B.M. / Skinner, C.F. / Watson, P.J. / Seaman, M.N.J. / Owen, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z2x.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z2x.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 1z2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/1z2x ftp://data.pdbj.org/pub/pdb/validation_reports/z2/1z2x | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | Biological unit is beleived to be monomer |
-Components
#1: Protein | Mass: 21626.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps29 / Plasmid: pGEX4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: Q9QZ88 #2: 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: 2.5 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris, 0.2M NaCl, 20% PEG3000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 16, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 21420 / % possible obs: 99.4 % / Observed criterion σ(I): 6.3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.08 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.3 / Rsym value: 0.252 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.22→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.463 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.204 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.347 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.224→2.281 Å / Total num. of bins used: 20 /
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