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- PDB-8ty9: KRAS 1-169 G12C Mutant at 313k -

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Basic information

Entry
Database: PDB / ID: 8ty9
TitleKRAS 1-169 G12C Mutant at 313k
ComponentsIsoform 2B of GTPase KRas
KeywordsHYDROLASE / GTPase
Function / homologysmall monomeric GTPase / Ca2+ pathway / GUANOSINE-5'-DIPHOSPHATE / Isoform 2B of GTPase KRas
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsDeck, S.L. / Xu, M. / Milano, S.K. / Aplin, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA201402 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM124166 United States
CitationJournal: To Be Published
Title: Temperature Gradient Structures of Oncogenic KRAS G12C Mutants
Authors: Deck, S.L. / Xu, M. / Aplin, C. / Milano, S.K.
History
DepositionAug 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7853
Polymers19,3181
Non-polymers4682
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.423, 41.740, 92.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19317.850 Da / Num. of mol.: 1 / Mutation: G12C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Plasmid: pDNA2.0 / Details (production host): Addgene Plasmid #111848 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01116-2, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200mM Na Acetate pH 3.6 100mM Tris pH 8.5 20% PEG 3350 1mM DTT

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Data collection

DiffractionMean temperature: 313 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.426→30.93 Å / Num. obs: 29134 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 16.98 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.183 / Net I/σ(I): 6.6
Reflection shellResolution: 1.426→1.45 Å / Rmerge(I) obs: 4.788 / Num. unique obs: 1423 / CC1/2: 0.404

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→30.93 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 1431 4.92 %
Rwork0.1919 --
obs0.1929 29103 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 29 115 1496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061403
X-RAY DIFFRACTIONf_angle_d1.1421898
X-RAY DIFFRACTIONf_dihedral_angle_d11.377197
X-RAY DIFFRACTIONf_chiral_restr0.099212
X-RAY DIFFRACTIONf_plane_restr0.011242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.480.35821380.34242711X-RAY DIFFRACTION99
1.48-1.540.32321300.29782736X-RAY DIFFRACTION100
1.54-1.610.29431200.25552746X-RAY DIFFRACTION100
1.61-1.690.26981500.24512723X-RAY DIFFRACTION100
1.69-1.80.29131500.2262729X-RAY DIFFRACTION100
1.8-1.930.26221510.19162733X-RAY DIFFRACTION100
1.93-2.130.20261440.18082765X-RAY DIFFRACTION100
2.13-2.440.22031400.17742779X-RAY DIFFRACTION100
2.44-3.070.19921350.19112827X-RAY DIFFRACTION100
3.07-30.930.17031730.15982923X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.4013 Å / Origin y: 2.0541 Å / Origin z: 11.1136 Å
111213212223313233
T0.1325 Å2-0.0054 Å20.0072 Å2-0.1289 Å2-0.0027 Å2--0.1316 Å2
L0.965 °2-0.0504 °20.1579 °2-0.7402 °2-0.1196 °2--0.9674 °2
S0.0131 Å °0.0405 Å °-0.053 Å °-0.0302 Å °-0.0087 Å °-0.0162 Å °0.0389 Å °0.0277 Å °-0 Å °
Refinement TLS groupSelection details: all

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