+Open data
-Basic information
Entry | Database: PDB / ID: 5wf9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Tepsin tENTH domain 1-153 | |||||||||
Components | AP-4 complex accessory subunit Tepsin | |||||||||
Keywords | PROTEIN TRANSPORT / protein trafficking | |||||||||
Function / homology | Function and homology information coated vesicle membrane / extrinsic component of organelle membrane / organelle membrane / trans-Golgi network membrane / intracellular membrane-bounded organelle / protein-containing complex binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Archuleta, T.L. / Jackson, L.P. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Traffic / Year: 2017 Title: Structure and evolution of ENTH and VHS/ENTH-like domains in tepsin. Authors: Archuleta, T.L. / Frazier, M.N. / Monken, A.E. / Kendall, A.K. / Harp, J. / McCoy, A.J. / Creanza, N. / Jackson, L.P. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5wf9.cif.gz | 61 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5wf9.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wf9_validation.pdf.gz | 403.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5wf9_full_validation.pdf.gz | 403.2 KB | Display | |
Data in XML | 5wf9_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 5wf9_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/5wf9 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/5wf9 | HTTPS FTP |
-Related structure data
Related structure data | 5wf1C 5wf2C 5wfbSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16866.463 Da / Num. of mol.: 1 / Fragment: UNP residues 1-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEPSIN, C17orf56, ENTHD2 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q96N21 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.45 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 150mM MES monohydrate pH 6.0, 15% (w/v) PEG6000. |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→63.8 Å / Num. obs: 16739 / % possible obs: 98.9 % / Redundancy: 26.8 % / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.02 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 17.4 % / Rmerge(I) obs: 1.905 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1518 / CC1/2: 0.534 / Rpim(I) all: 0.462 / % possible all: 91.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WFB Resolution: 1.8→45.09 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→45.09 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|