+Open data
-Basic information
Entry | Database: PDB / ID: 6md5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of zebrafish Vps26A | ||||||
Components | Vacuolar protein sorting-associated protein 26AVacuole | ||||||
Keywords | ENDOCYTOSIS / retromer / vps26 / endoscope | ||||||
Function / homology | Function and homology information WNT ligand biogenesis and trafficking / retromer complex / retrograde transport, endosome to Golgi / intracellular protein transport / vesicle / early endosome / endosome membrane / endosome / cytosol Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Collins, B.M. / Leneva, N. | ||||||
Citation | Journal: To Be Published Title: TBA Authors: Collins, B.M. / Leneva, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6md5.cif.gz | 185.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6md5.ent.gz | 149.2 KB | Display | PDB format |
PDBx/mmJSON format | 6md5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/6md5 ftp://data.pdbj.org/pub/pdb/validation_reports/md/6md5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2fauS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37379.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: vps26a, zgc:56673 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TNP8 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2 M Ammonium sulfate, 0.1 M Bis-tris pH 5.5, 25 %(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→26.4 Å / Num. obs: 34105 / % possible obs: 100 % / Redundancy: 14.1 % / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1808 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FAU Resolution: 1.7→26.4 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.25
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→26.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|