+Open data
-Basic information
Entry | Database: PDB / ID: 5cj2 | ||||||
---|---|---|---|---|---|---|---|
Title | Ran GDP Y39A mutant triclinic crystal form | ||||||
Components | GTP-binding nuclear protein Ran | ||||||
Keywords | HYDROLASE / GTPase / nuclear transport / transport protein | ||||||
Function / homology | Function and homology information RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein ...RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / dynein intermediate chain binding / ribosomal subunit export from nucleus / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / sperm flagellum / nuclear pore / protein export from nucleus / centriole / viral process / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / mitotic cell cycle / nuclear envelope / positive regulation of protein binding / midbody / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / cell division / protein domain specific binding / GTPase activity / chromatin binding / chromatin / GTP binding / nucleolus / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Vetter, I.R. / Brucker, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy. Authors: Rudack, T. / Jenrich, S. / Brucker, S. / Vetter, I.R. / Gerwert, K. / Kotting, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5cj2.cif.gz | 335.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5cj2.ent.gz | 281.4 KB | Display | PDB format |
PDBx/mmJSON format | 5cj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/5cj2 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/5cj2 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
-Components
#1: Protein | Mass: 24364.008 Da / Num. of mol.: 8 / Mutation: Y39A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET3d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826 #2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.78 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 35% PEG 1000, 50mM Tris pH 8.5, 20mM MgCl2, 1 mM BeF |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999989 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 19, 2009 |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999989 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→47.579 Å / Num. obs: 156462 / % possible obs: 92.2 % / Redundancy: 2.02 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.42 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 1.73 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.46 / % possible all: 81.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: human Ran GDP Resolution: 1.75→47.579 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.89 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 29.118 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→47.579 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|