+Open data
-Basic information
Entry | Database: PDB / ID: 6naz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of DIRAS 2/3 chimera in complex with GDP | |||||||||
Components | GTP-binding protein Di-Ras2,GTP-binding protein Di-Ras3,GTP-binding protein Di-Ras2 | |||||||||
Keywords | TRANSPORT PROTEIN / Biological activity | |||||||||
Function / homology | Function and homology information : / small GTPase-mediated signal transduction / regulation of cyclin-dependent protein serine/threonine kinase activity / GDP binding / GTPase activity / GTP binding / signal transduction / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.081 Å | |||||||||
Authors | Gilbert, Y.H. / Reger, A. / Sharma, R. / Bast, J. / Kim, C. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: To Be Published Title: Crystal structure of DIRAS 2/3 chimera in complex with GDP Authors: Gilbert, Y.H. / Reger, A. / Sharma, R. / Bast, C.R. / Kim, C. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6naz.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6naz.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 6naz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/6naz ftp://data.pdbj.org/pub/pdb/validation_reports/na/6naz | HTTPS FTP |
---|
-Related structure data
Related structure data | 2erxS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 22495.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DIRAS2, DIRAS3, ARHI, NOEY2, RHOI / Production host: Escherichia coli (E. coli) / References: UniProt: Q96HU8, UniProt: O95661 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-GDP / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.68 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1500 mM Ammonium sulfate, 100 mM Tris base/Hydrochloric acid pH 8.5, 12% glycerol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→79.7 Å / Num. obs: 4324 / % possible obs: 99.98 % / Redundancy: 13.3 % / Net I/σ(I): 2.6 |
Reflection shell | Resolution: 3.08→3.19 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ERX Resolution: 3.081→79.7 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.52 / 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: 3.081→79.7 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.0814→79.727 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 41.269 Å / Origin y: 51.6889 Å / Origin z: 7.1475 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |