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- PDB-8txk: KRAS 1-169 G12C Mutant at 240k -

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Basic information

Entry
Database: PDB / ID: 8txk
TitleKRAS 1-169 G12C Mutant at 240k
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: 1.38 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 23, 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
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.322, 42.368, 93.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 146 / 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: 2.01 Å3/Da / Density % sol: 38.92 %
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: 240 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: 1.38→36.26 Å / Num. obs: 31196 / % possible obs: 94.9 % / Redundancy: 12 % / Biso Wilson estimate: 13.81 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.2
Reflection shellResolution: 1.38→1.404 Å / Num. unique obs: 1112 / CC1/2: 0.362

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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: 1.38→36.24 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 1518 4.87 %
Rwork0.1949 --
obs0.1962 31193 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→36.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 29 146 1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061403
X-RAY DIFFRACTIONf_angle_d1.0041898
X-RAY DIFFRACTIONf_dihedral_angle_d10.606197
X-RAY DIFFRACTIONf_chiral_restr0.088212
X-RAY DIFFRACTIONf_plane_restr0.007242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.430.33851040.32332033X-RAY DIFFRACTION73
1.43-1.480.27161220.28672618X-RAY DIFFRACTION94
1.48-1.540.28041190.24332698X-RAY DIFFRACTION96
1.54-1.60.23921430.22592701X-RAY DIFFRACTION96
1.6-1.690.24011600.21882697X-RAY DIFFRACTION96
1.69-1.80.26291360.2172742X-RAY DIFFRACTION97
1.8-1.930.23971130.20852790X-RAY DIFFRACTION98
1.93-2.130.23081410.19682765X-RAY DIFFRACTION98
2.13-2.440.23151310.19412812X-RAY DIFFRACTION98
2.44-3.070.24261780.19682827X-RAY DIFFRACTION99
3.07-36.240.16921710.15462992X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.6795 Å / Origin y: 2.9619 Å / Origin z: 11.3897 Å
111213212223313233
T0.0853 Å20.0016 Å20.0046 Å2-0.0693 Å2-0.0031 Å2--0.0805 Å2
L1.4447 °2-0.152 °2-0.0481 °2-1.0966 °2-0.3668 °2--1.8521 °2
S0.021 Å °0.0155 Å °-0.0376 Å °-0.0443 Å °-0.0176 Å °-0.0184 Å °0.0813 Å °0.0518 Å °-0.0051 Å °
Refinement TLS groupSelection details: all

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