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- PDB-7w5r: KRAS G12V and peptide complex -

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Basic information

Entry
Database: PDB / ID: 7w5r
TitleKRAS G12V and peptide complex
Components
  • Isoform 2B of GTPase KRas
  • LEU-TYR-ASP-VAL-ALA
KeywordsSTRUCTURAL PROTEIN / Kras / hrev107
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: 3.87 Å
AuthorsKim, H.J. / Han, C.W. / Jang, S.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural basis of the oncogenic KRAS mutant and GJ101 complex.
Authors: Kim, H.J. / Han, C.W. / Jeong, M.S. / Jang, S.B.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
E: Isoform 2B of GTPase KRas
H: LEU-TYR-ASP-VAL-ALA
I: Isoform 2B of GTPase KRas
M: Isoform 2B of GTPase KRas
Q: Isoform 2B of GTPase KRas
U: Isoform 2B of GTPase KRas
X: LEU-TYR-ASP-VAL-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,04620
Polymers121,2418
Non-polymers2,80512
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-136 kcal/mol
Surface area44130 Å2
Unit cell
Length a, b, c (Å)40.556, 82.513, 82.573
Angle α, β, γ (deg.)119.986, 90.061, 90.015
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 20013.539 Da / Num. of mol.: 6 / Mutation: G12V
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) / Strain (production host): BL21(DE3) / References: UniProt: P01116-2, small monomeric GTPase
#2: Protein/peptide LEU-TYR-ASP-VAL-ALA


Mass: 579.643 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: polyethylene glycol 3350, 0.2 M potassium nitrate at pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.87→50 Å / Num. obs: 8581 / % possible obs: 99.64 % / Redundancy: 3.8 % / Biso Wilson estimate: 77.13 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.3
Reflection shellResolution: 3.87→3.95 Å / Rmerge(I) obs: 0.1838 / Num. unique obs: 2674

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-20001.14_3260data collection
Cootmodel building
HKL-2000data reduction
CCP4idata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UQW

5uqw


Resolution: 3.87→35.76 Å / SU ML: 0.5682 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 34.855
RfactorNum. reflection% reflection
Rfree0.3102 437 5.09 %
Rwork0.2233 8145 -
obs0.2277 8447 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.68 Å2
Refinement stepCycle: LAST / Resolution: 3.87→35.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7588 0 174 0 7762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00527886
X-RAY DIFFRACTIONf_angle_d0.991810673
X-RAY DIFFRACTIONf_chiral_restr0.05141219
X-RAY DIFFRACTIONf_plane_restr0.0051348
X-RAY DIFFRACTIONf_dihedral_angle_d8.43174737
LS refinement shellResolution: 3.87→3.95 Å
RfactorNum. reflection% reflection
Rfree0.2445 173 -
Rwork0.1848 2674 -
obs--99.13 %
Refinement TLS params.Method: refined / Origin x: 9.71337819261 Å / Origin y: -19.2138395566 Å / Origin z: 25.4119434274 Å
111213212223313233
T0.135935054444 Å20.00425677061533 Å20.0103448416971 Å2-0.121508069066 Å2-0.000296125090882 Å2--0.153076768736 Å2
L0.042048240167 °2-0.00241758894174 °20.0385335171883 °2-0.00592697486144 °2-0.0171105963666 °2--0.0540502975693 °2
S0.0164337402089 Å °0.0261495907643 Å °0.0289564268201 Å °-0.0293258563132 Å °0.0109767705516 Å °-0.0168640801727 Å °0.0158792924931 Å °0.0153205592829 Å °0.0281082737367 Å °
Refinement TLS groupSelection details: all

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