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Yorodumi- PDB-3lh9: Crystal structure of mouse VPS26B(L197S/R199E) in spacegroup P41 21 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lh9 | ||||||
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Title | Crystal structure of mouse VPS26B(L197S/R199E) in spacegroup P41 21 2 | ||||||
Components | Vacuolar protein sorting-associated protein 26BVacuole | ||||||
Keywords | PROTEIN TRANSPORT / arrestin / fibronectin / Membrane / Transport | ||||||
Function / homology | Function and homology information retromer complex / retrograde transport, endosome to Golgi / phagocytic vesicle / intracellular protein transport / cellular response to type II interferon / late endosome / early endosome / endosome / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Collins, B. / Shaw, D. / Norwood, S. | ||||||
Citation | Journal: Traffic / Year: 2011 Title: Assembly and solution structure of the core retromer protein complex. Authors: Norwood, S.J. / Shaw, D.J. / Cowieson, N.P. / Owen, D.J. / Teasdale, R.D. / Collins, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lh9.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lh9.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/3lh9 ftp://data.pdbj.org/pub/pdb/validation_reports/lh/3lh9 | HTTPS FTP |
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-Related structure data
Related structure data | 3lh8C 3lhaC 2r51S S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39648.973 Da / Num. of mol.: 2 / Fragment: UNP residues 7-336 / Mutation: L197S,R199E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8C0E2 #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: 4.74 Å3/Da / Density % sol: 74.03 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2M sodium formate, 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: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364 Å |
Detector | Detector: CCD / Date: Nov 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95364 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.2 Å / Num. obs: 60249 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 62.8 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 3 / Num. unique all: 5584 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R51 Resolution: 2.4→42.541 Å / SU ML: 0.34 / σ(F): 1.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.914 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→42.541 Å
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Refine LS restraints |
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LS refinement shell |
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