+Open data
-Basic information
Entry | Database: PDB / ID: 7w5r | ||||||
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Title | KRAS G12V and peptide complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Kras / hrev107 | ||||||
Function / homology | small monomeric GTPase / Ca2+ pathway / GUANOSINE-5'-DIPHOSPHATE / Isoform 2B of GTPase KRas Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.87 Å | ||||||
Authors | Kim, H.J. / Han, C.W. / Jang, S.B. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Structural basis of the oncogenic KRAS mutant and GJ101 complex. Authors: Kim, H.J. / Han, C.W. / Jeong, M.S. / Jang, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w5r.cif.gz | 471 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w5r.ent.gz | 319.7 KB | Display | PDB format |
PDBx/mmJSON format | 7w5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w5r_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7w5r_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7w5r_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 7w5r_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/7w5r ftp://data.pdbj.org/pub/pdb/validation_reports/w5/7w5r | HTTPS FTP |
-Related structure data
Related structure data | 5uqwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20013.539 Da / Num. of mol.: 6 / Mutation: G12V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01116-2, small monomeric GTPase #2: Protein/peptide | Mass: 579.643 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GDP / Has ligand of interest | N | |
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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: 2.11 Å3/Da / Density % sol: 41.58 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: polyethylene glycol 3350, 0.2 M potassium nitrate at pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.87→50 Å / Num. obs: 8581 / % possible obs: 99.64 % / Redundancy: 3.8 % / Biso Wilson estimate: 77.13 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 3.87→3.95 Å / Rmerge(I) obs: 0.1838 / Num. unique obs: 2674 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UQW Resolution: 3.87→35.76 Å / SU ML: 0.5682 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 34.855
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.68 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.87→35.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.87→3.95 Å
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Refinement TLS params. | Method: refined / Origin x: 9.71337819261 Å / Origin y: -19.2138395566 Å / Origin z: 25.4119434274 Å
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Refinement TLS group | Selection details: all |