+Open data
-Basic information
Entry | Database: PDB / ID: 7xkj | ||||||
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Title | Kras-G12D-GDP-MRTX1133 by FIB-MicroED | ||||||
Components | KRAS proto-oncogene, GTPase | ||||||
Keywords | ONCOPROTEIN / g12d / gdp / gtpase / hydrolase-hydrolase inhibitor complex / hydrolase/hydrolase inhibitor / MicroED | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3 Å | ||||||
Authors | Li, X.M. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Kras-G12D-GDP-MRTX1133 by FIB-MicroED Authors: Li, X.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xkj.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xkj.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xkj_validation.pdf.gz | 566.4 KB | Display | wwPDB validaton report |
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Full document | 7xkj_full_validation.pdf.gz | 572.6 KB | Display | |
Data in XML | 7xkj_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 7xkj_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/7xkj ftp://data.pdbj.org/pub/pdb/validation_reports/xk/7xkj | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19313.730 Da / Num. of mol.: 1 / Mutation: G12D, C118S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: mMyoMyo1_007468 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J7Z4L6 |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-6IC / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: Isoform 2B of GTPase KRas GUANOSINE-5'-DIPHOSPHATE 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d] ...Name: Isoform 2B of GTPase KRas GUANOSINE-5'-DIPHOSPHATE 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol MAGNESIUM ION Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.02 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Data collection
Microscopy | Model: JEOL 2100F |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION / Nominal magnification: 6000 X / Calibrated magnification: 6000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2300 nm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FISCHIONE 2550 / Temperature (max): 100 K / Temperature (min): 90 K |
Image recording | Average exposure time: 2 sec. / Electron dose: 0.02 e/Å2 / Detector mode: OTHER / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) |
EM imaging optics | Phase plate: OTHER |
EM diffraction | Camera length: 100 mm |
EM diffraction shell | Resolution: 3→33.17 Å / Fourier space coverage: 100 % / Multiplicity: 8.3 / Num. of structure factors: 3591 / Phase residual: 13.5 ° |
EM diffraction stats | Fourier space coverage: 100 % / High resolution: 3 Å / Num. of intensities measured: 29866 / Num. of structure factors: 3591 / Phase error rejection criteria: no / Rmerge: 0.4827 |
Diffraction source | Wavelength: 0.025 |
Radiation wavelength | Wavelength: 0.025 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 44.23 Å2 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158 / Classification: refinement / Contact author: Paul D. Adams / Contact author email: pdadams[at]lbl.gov / Language: Python/C++ / URL: https://www.phenix-online.org/ / Type: program | ||||||||||||||||||||||||||||||||||||||||||
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EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 39.868 Å / B: 51.757 Å / C: 89.611 Å / Space group name: P212121 / Space group num: 19 | ||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: CRYSTALLOGRAPHY / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 200 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient / Details: no | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7RPZ Pdb chain-ID: A / Pdb chain residue range: 1-169 | ||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3→35.51 Å / SU ML: 0.3835 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2454 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 30.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→35.51 Å
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Refine LS restraints |
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LS refinement shell |
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