+Open data
-Basic information
Entry | Database: PDB / ID: 1z6y | ||||||
---|---|---|---|---|---|---|---|
Title | Structure Of Human ADP-Ribosylation Factor-Like 5 | ||||||
Components | ADP-ribosylation factor-like protein 5 | ||||||
Keywords | TRANSPORT PROTEIN / GDP-Binding / Membrane Trafficking / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information protein localization to Golgi membrane / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / GTPase activity / GTP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Choe, J. / Atanassova, A. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Structure Of Human ADP-Ribosylation Factor-Like 5 Authors: Atanassova, A. / Choe, J. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Bochkarev, A. / Park, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1z6y.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1z6y.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 1z6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/1z6y ftp://data.pdbj.org/pub/pdb/validation_reports/z6/1z6y | HTTPS FTP |
---|
-Related structure data
Related structure data | 1rrfS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20752.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARL5, ARFLP5 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y689 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: PEG 4000, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 5, 2005 / Details: CONFOCAL MAXFLUX |
Radiation | Monochromator: CONFOCAL MAXFLUX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50.9 Å / Num. all: 13917 / Num. obs: 13917 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 5 / % possible all: 95 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RRF Resolution: 2.4→50.9 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / ESU R: 0.81 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.023 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
|