[English] 日本語
Yorodumi- PDB-2oxr: PAB0955 crystal structure : a GTPase in GDP and Mg bound form fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oxr | ||||||
---|---|---|---|---|---|---|---|
Title | PAB0955 crystal structure : a GTPase in GDP and Mg bound form from Pyrococcus abyssi (after GTP hydrolysis) | ||||||
Components | ATP(GTP)binding protein | ||||||
Keywords | HYDROLASE / GTP binding protein / GTPase / P-loop / Rossmann fold / GDP | ||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Gras, S. / Carpentier, P. / Armengaud, J. / Housset, D. | ||||||
Citation | Journal: Embo Rep. / Year: 2007 Title: Structural insights into a new homodimeric self-activated GTPase family. Authors: Gras, S. / Chaumont, V. / Fernandez, B. / Carpentier, P. / Charrier-Savournin, F. / Schmitt, S. / Pineau, C. / Flament, D. / Hecker, A. / Forterre, P. / Armengaud, J. / Housset, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2oxr.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2oxr.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 2oxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/2oxr ftp://data.pdbj.org/pub/pdb/validation_reports/ox/2oxr | HTTPS FTP |
---|
-Related structure data
Related structure data | 1yr6C 1yr7C 1yr8C 1yr9C 1yraC 1yrbSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30334.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: pab0955 / Plasmid: pCRT7/NT-topo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys / References: UniProt: Q9UYR9 |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 38.7314 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 5.6 Details: 0.1M tri-Na citrate pH 5.6, 15% PEG 4000, 0.2M ammonium acetate, 20mM DTT, 0.65mM GTP, 8mg/ml protein, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Feb 26, 2004 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 9973 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rsym value: 0.067 / Net I/σ(I): 19.55 |
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 5.76 / Rsym value: 0.404 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YRB Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.9275 / Cor.coef. Fo:Fc free: 0.875 / Isotropic thermal model: isotropic / σ(F): 0 / ESU R: 0.617 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.15 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.48 Å / Total num. of bins used: 15
|