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Yorodumi- PDB-1yrb: PAB0955 crystal structure : a GTPase in GDP and Mg bound form fro... -
+Open data
-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 | ||||||
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: 1.75 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. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yrb.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yrb.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 1yrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/1yrb ftp://data.pdbj.org/pub/pdb/validation_reports/yr/1yrb | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer, which is present in the asymmetric unit |
-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.) Pyrococcus abyssi (archaea) / Gene: PAB0955 / Plasmid: pCRT7/NT-topo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys / References: GenBank: 5458856, UniProt: Q9UYR9*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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