+Open data
-Basic information
Entry | Database: PDB / ID: 1w24 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Of human Vps29 | ||||||
Components | VACUOLAR PROTEIN SORTING PROTEIN 29Vacuole | ||||||
Keywords | CYTOPLASMIC PROTEIN / VACUOLAR PROTEIN SORTING PROTEIN / ALPHA-BETA-BETA-ALPHA SANDWICH | ||||||
Function / homology | Function and homology information retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / early endosome / endosome membrane / endosome ...retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / early endosome / endosome membrane / endosome / intracellular membrane-bounded organelle / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.1 Å | ||||||
Authors | Wang, D. / Guo, M. / Teng, M. / Niu, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal Structure of Human Vacuolar Protein Sorting Protein 29 Reveals a Phosphodiesterase/Nuclease-Like Fold and Two Protein-Protein Interaction Sites. Authors: Wang, D. / Guo, M. / Liang, Z. / Fan, J. / Zhu, Z. / Zang, J. / Zhu, Z. / Li, X. / Teng, M. / Niu, L. / Dong, Y. / Liu, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1w24.cif.gz | 44.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1w24.ent.gz | 34.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/1w24 ftp://data.pdbj.org/pub/pdb/validation_reports/w2/1w24 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 20531.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBQ0 |
---|---|
#2: Water | ChemComp-HOH / |
Compound details | FUNCTION: POSSIBLE ROLE IN VESICULAR PROTEIN SORTING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 46 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 Details: 25%PEG4000, 10%ETHYENE GLYCOL, 100MM HEPES PH7.5, pH 7.50 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 2004 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 10937 / % possible obs: 96.5 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.05 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / % possible all: 95.5 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Num. obs: 10686 / Redundancy: 4.97 % / Num. measured all: 54013 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 95.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.1→14.94 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 36.23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→14.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|