+Open data
-Basic information
Entry | Database: PDB / ID: 2g3y | ||||||
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Title | Crystal structure of the human small GTPase GEM | ||||||
Components | GTP-binding protein GEM | ||||||
Keywords | SIGNALING PROTEIN / GEM / small GTPase / GDP / inactive state / RGK family / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information metaphase chromosome alignment / calcium channel regulator activity / chromosome organization / spindle midzone / NPAS4 regulates expression of target genes / mitotic spindle / cytoplasmic side of plasma membrane / GDP binding / mitotic cell cycle / midbody ...metaphase chromosome alignment / calcium channel regulator activity / chromosome organization / spindle midzone / NPAS4 regulates expression of target genes / mitotic spindle / cytoplasmic side of plasma membrane / GDP binding / mitotic cell cycle / midbody / cell surface receptor signaling pathway / calmodulin binding / immune response / GTPase activity / GTP binding / magnesium ion binding / signal transduction / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ugochukwu, E. / Soundararajan, M. / Elkins, J. / Gileadi, C. / Schoch, G. / Sobott, F. / Fedorov, O. / Bray, J. / Pantic, N. / Berridge, G. ...Ugochukwu, E. / Soundararajan, M. / Elkins, J. / Gileadi, C. / Schoch, G. / Sobott, F. / Fedorov, O. / Bray, J. / Pantic, N. / Berridge, G. / Burgess, N. / Lee, W.H. / Turnbull, A. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Doyle, D. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the human small GTPase GEM Authors: Ugochukwu, E. / Soundararajan, M. / Elkins, J. / Schoch, G. / Gileadi, C. / Doyle, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g3y.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g3y.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 2g3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/2g3y ftp://data.pdbj.org/pub/pdb/validation_reports/g3/2g3y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23854.738 Da / Num. of mol.: 1 / Fragment: GEM Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GEM, KIR / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-R3 / References: UniProt: P55040 |
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#2: Chemical | ChemComp-GDP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: PEG3350, Ammonium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 11803 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.25→2.37 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RAP, 1KAO Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.649 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -6.7295 Å / Origin y: 3.5538 Å / Origin z: -15.5265 Å
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