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Yorodumi- PDB-3c5c: Crystal structure of human Ras-like, family 12 protein in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c5c | ||||||
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Title | Crystal structure of human Ras-like, family 12 protein in complex with GDP | ||||||
Components | RAS-like protein 12 | ||||||
Keywords | SIGNALING PROTEIN / ras / rasl12 / gdp / gtpase / Structural Genomics Consortium / SGC / limited proteolysis / GTP-binding / Nucleotide-binding | ||||||
Function / homology | Function and homology information small monomeric GTPase / GDP binding / GTPase activity / GTP binding / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Shen, L. / Tong, Y. / Tempel, W. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human Ras-like, family 12 protein in complex with GDP. Authors: Shen, L. / Tong, Y. / Tempel, W. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c5c.cif.gz | 152.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c5c.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 3c5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c5c_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3c5c_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3c5c_validation.xml.gz | 28 KB | Display | |
Data in CIF | 3c5c_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/3c5c ftp://data.pdbj.org/pub/pdb/validation_reports/c5/3c5c | HTTPS FTP |
-Related structure data
Related structure data | 2atvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
#1: Protein | Mass: 21430.076 Da / Num. of mol.: 4 / Fragment: Residues 18-186 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RASL12, RIS / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9NYN1 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GDP / #4: Chemical | #5: 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: 1.86 Å3/Da / Density % sol: 33.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 Details: 0.1 M Tris-HCl pH 8.5, 28% PEG 4000, 0.2 M Magnesium chloride. In situ proteolysis with 1:100 endoproteinase Glu-C V8, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 18, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→40 Å / Num. obs: 52667 / % possible obs: 98.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.119 / Χ2: 1.501 / Net I/σ(I): 7.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2ATV Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.186 / SU B: 3.89 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs coot, molprobity, ffas03, SCWRL have also been used in refinement
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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: 18.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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