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- PDB-2oxr: PAB0955 crystal structure : a GTPase in GDP and Mg bound form fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oxr | ||||||
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Title | PAB0955 crystal structure : a GTPase in GDP and Mg bound form from Pyrococcus abyssi (after GTP hydrolysis) | ||||||
![]() | ATP(GTP)binding protein | ||||||
![]() | HYDROLASE / GTP binding protein / GTPase / P-loop / Rossmann fold / GDP | ||||||
Function / homology | ![]() Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gras, S. / Carpentier, P. / Armengaud, J. / Housset, D. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.4 KB | Display | ![]() |
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PDB format | ![]() | 48.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1yr6C ![]() 1yr7C ![]() 1yr8C ![]() 1yr9C ![]() 1yraC ![]() 1yrbSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30334.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 38.7314 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.48 Å / Total num. of bins used: 15
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