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Yorodumi- PDB-7ok3: Crystal Structure of KRasG13C in Complex with Nucleotide-based Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ok3 | |||||||||
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Title | Crystal Structure of KRasG13C in Complex with Nucleotide-based Covalent Inhibitor edaGDP | |||||||||
Components | Isoform 2B of GTPase KRas | |||||||||
Keywords | HYDROLASE / GTPase / Ras / KRas / KRasG13C / Nucleotide analogues / edaGDP | |||||||||
Function / homology | small monomeric GTPase / Ca2+ pathway / edaGDP / Isoform 2B of GTPase KRas Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Goebel, L. / Mueller, M.P. / Rauh, D. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Elife / Year: 2023 Title: Targeting oncogenic KRasG13C with nucleotide-based covalent inhibitors. Authors: Goebel, L. / Kirschner, T. / Koska, S. / Rai, A. / Janning, P. / Maffini, S. / Vatheuer, H. / Czodrowski, P. / Goody, R.S. / Muller, M.P. / Rauh, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ok3.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ok3.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ok3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ok3_validation.pdf.gz | 881.4 KB | Display | wwPDB validaton report |
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Full document | 7ok3_full_validation.pdf.gz | 881.6 KB | Display | |
Data in XML | 7ok3_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 7ok3_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/7ok3 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/7ok3 | HTTPS FTP |
-Related structure data
Related structure data | 7ok4C 4obeS S: Starting model for refinement C: citing same article (ref.) |
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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: 19433.881 Da / Num. of mol.: 1 / Mutation: G13C 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) / References: UniProt: P01116-2, small monomeric GTPase |
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#2: Chemical | ChemComp-VJ8 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M (NH4)F, 20 % PEG3350, 67 mg/mL KRasG13C-edaGDP, 0.1 uL reservoir + 0.1 uL protein solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.915 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→41.243 Å / Num. obs: 22009 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.103 / Net I/σ(I): 12.71 |
Reflection shell | Resolution: 1.6→1.7 Å / Rmerge(I) obs: 0.966 / Num. unique obs: 3625 / CC1/2: 0.801 / Rrim(I) all: 1.016 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OBE Resolution: 1.6→41.24 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.09 / Stereochemistry target values: ML
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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 max: 83.76 Å2 / Biso mean: 27.867 Å2 / Biso min: 13.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→41.24 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 55.4797 Å / Origin y: 20.7789 Å / Origin z: 12.1359 Å
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Refinement TLS group |
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