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- PDB-1yrb: 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: 1yrb | ||||||
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Title | PAB0955 crystal structure : a GTPase in GDP and Mg bound form from Pyrococcus abyssi | ||||||
![]() | 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. #1: ![]() Title: Expression, purification, crystallization and preliminary crystallographic analysis of the PAB0955 gene product Authors: Gras, S. / Fernandez, B. / Chaumont, V. / Carpentier, 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 | ![]() | 131.1 KB | Display | ![]() |
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PDB format | ![]() | 101.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1yr6SC ![]() 1yr7C ![]() 1yr8C ![]() 1yr9C ![]() 1yraC ![]() 2oxrC 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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Unit cell |
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Details | The biological assembly is a dimer, which is present in the asymmetric unit |
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Components
#1: Protein | Mass: 30334.795 Da / Num. of mol.: 2 / Fragment: residues 1-248 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 13% PEG4000, 20mM DTT, 10% glycerol, 50mM NaCl, 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 0.65mM GDP, 1mM WO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2004 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 60611 / Num. obs: 59865 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 27.296 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 12.47 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 5.91 / Num. unique all: 4813 / Rsym value: 0.372 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YR6 Resolution: 1.75→15 Å / Cor.coef. Fo:Fc: 0.963 / SU B: 2.209 / SU ML: 0.072 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.118 / 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: 33.883 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.751→1.812 Å / Total num. of bins used: 15
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