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- PDB-8tvk: KRAS 1-169 G12C Mutant at 100k -

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Basic information

Entry
Database: PDB / ID: 8tvk
TitleKRAS 1-169 G12C Mutant at 100k
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: 1.04 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: Biorxiv / Year: 2025
Title: Revealing Functional Hotspots: Temperature-Dependent Crystallography of K-RAS Highlights Allosteric and Druggable Sites.
Authors: Deck, S.L. / Xu, M. / Milano, S.K. / Cerione, R.A.
History
DepositionAug 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 26, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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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
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.022, 40.545, 91.383
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 / 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: isolated from a natural source / 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.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.87 Å3/Da / Density % sol: 34.39 %
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: 100 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: Aug 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.04→29.67 Å / Num. obs: 66735 / % possible obs: 94.65 % / Redundancy: 8.2 % / CC1/2: 0.998 / Net I/σ(I): 7.4
Reflection shellResolution: 1.04→1.077 Å / Num. unique obs: 4345 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.04→29.67 Å / SU ML: 0.11 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 3275 4.91 %
Rwork0.1873 --
obs0.1882 66735 94.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.04→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 29 247 1628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d1.0371898
X-RAY DIFFRACTIONf_dihedral_angle_d11.423197
X-RAY DIFFRACTIONf_chiral_restr0.078212
X-RAY DIFFRACTIONf_plane_restr0.008242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.060.4029660.36371591X-RAY DIFFRACTION55
1.06-1.070.3114950.32691895X-RAY DIFFRACTION66
1.07-1.090.30071220.31042190X-RAY DIFFRACTION77
1.09-1.110.3171030.28552496X-RAY DIFFRACTION86
1.11-1.130.28221330.26112704X-RAY DIFFRACTION93
1.13-1.150.23761580.24172818X-RAY DIFFRACTION98
1.15-1.170.22811720.21522844X-RAY DIFFRACTION99
1.17-1.20.2141460.19832889X-RAY DIFFRACTION100
1.2-1.230.21521280.19922921X-RAY DIFFRACTION100
1.23-1.260.21531230.19822907X-RAY DIFFRACTION100
1.26-1.290.19921680.19312862X-RAY DIFFRACTION100
1.29-1.330.21541420.18982898X-RAY DIFFRACTION100
1.33-1.370.19941580.19622900X-RAY DIFFRACTION100
1.37-1.420.19941660.18362872X-RAY DIFFRACTION100
1.42-1.480.18211580.18142907X-RAY DIFFRACTION100
1.48-1.550.18731600.17572909X-RAY DIFFRACTION100
1.55-1.630.21591600.17952939X-RAY DIFFRACTION100
1.63-1.730.19721420.18252912X-RAY DIFFRACTION100
1.73-1.860.21861580.1862937X-RAY DIFFRACTION100
1.86-2.050.18541570.17992935X-RAY DIFFRACTION100
2.05-2.350.19511510.17572982X-RAY DIFFRACTION100
2.35-2.960.21611430.18433017X-RAY DIFFRACTION100
2.96-29.670.17971660.163135X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.3612 Å / Origin y: 1.8486 Å / Origin z: -10.655 Å
111213212223313233
T0.0717 Å20.0029 Å20.0018 Å2-0.0647 Å2-0.0016 Å2--0.0703 Å2
L0.6971 °2-0.0008 °2-0.0176 °2-0.4026 °20.0475 °2--0.6661 °2
S0.0021 Å °-0.0014 Å °-0.0087 Å °0.0026 Å °-0.0005 Å °0.0009 Å °0.0209 Å °-0.0194 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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