+Open data
-Basic information
Entry | Database: PDB / ID: 3kkq | ||||||
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Title | Crystal structure of M-Ras P40D in complex with GDP | ||||||
Components | Ras-related protein M-Ras | ||||||
Keywords | SIGNALING PROTEIN / GTP-binding / GTPase | ||||||
Function / homology | Function and homology information RAF activation / GTP-dependent protein binding / cellular response to leukemia inhibitory factor / small monomeric GTPase / G protein activity / GDP binding / Ras protein signal transduction / GTPase activity / GTP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å | ||||||
Authors | Muraoka, S. / Shima, F. / Liao, J. / Ijiri, Y. / Matsumoto, K. / Ye, M. / Inoue, T. / Kataoka, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural basis for conformational dynamics of GTP-bound Ras protein Authors: Shima, F. / Ijiri, Y. / Muraoka, S. / Liao, J. / Ye, M. / Araki, M. / Matsumoto, K. / Yamamoto, N. / Sugimoto, T. / Yoshikawa, Y. / Kumasaka, T. / Yamamoto, M. / Tamura, A. / Kataoka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kkq.cif.gz | 56.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kkq.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 3kkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/3kkq ftp://data.pdbj.org/pub/pdb/validation_reports/kk/3kkq | HTTPS FTP |
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-Related structure data
Related structure data | 3kkmC 3kknC 3kkoC 3kkpC 1x1rS 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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Components on special symmetry positions |
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Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
#1: Protein | Mass: 20854.705 Da / Num. of mol.: 1 / Fragment: G domain, UNP residues 1-178 / Mutation: P40D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): AG-1 / References: UniProt: O08989 |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
#4: 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: 48.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG-4000, sodium acetate, ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2005 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→36.11 Å / Num. all: 62215 / Num. obs: 62215 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8859 / Rsym value: 0.286 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1X1R Resolution: 1.2→29.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.466 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.329 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→29.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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