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Yorodumi- PDB-7f0w: Crystal structure of KRAS-G12D bound to GDP with switch 1 open co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f0w | ||||||
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Title | Crystal structure of KRAS-G12D bound to GDP with switch 1 open conformation | ||||||
Components | Isoform 2B of GTPase KRas | ||||||
Keywords | SIGNALING PROTEIN / GTPase | ||||||
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: 1.39 Å | ||||||
Authors | Zhang, F. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of KRAS-G12D bound to GDP with switch 1 open conformation Authors: Zhang, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f0w.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f0w.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 7f0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f0w_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7f0w_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7f0w_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 7f0w_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/7f0w ftp://data.pdbj.org/pub/pdb/validation_reports/f0/7f0w | HTTPS FTP |
-Related structure data
Related structure data | 4obeS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 19285.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116-2, small monomeric GTPase |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
#4: 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: 2.57 Å3/Da / Density % sol: 52.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 1.0 M sodium citrate, 0.1M Tris pH 7.0, 0.2M NaCl |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9 Å |
Detector | Type: AGILENT EOS CCD / Detector: CCD / Date: Apr 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→29 Å / Num. obs: 43707 / % possible obs: 99.6 % / Redundancy: 18.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.039 / Rrim(I) all: 0.123 / Net I/av σ(I): 0.65 / Net I/σ(I): 11.25 |
Reflection shell | Resolution: 1.35→1.39 Å / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3086 / CC1/2: 0.818 / Rpim(I) all: 0.259 / Rrim(I) all: 0.982 / Χ2: 0.22 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4obe Resolution: 1.39→22.76 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 23.36 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→22.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.392→1.442 Å
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