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- PDB-7ok3: Crystal Structure of KRasG13C in Complex with Nucleotide-based Co... -

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Basic information

Entry
Database: PDB / ID: 7ok3
TitleCrystal Structure of KRasG13C in Complex with Nucleotide-based Covalent Inhibitor edaGDP
ComponentsIsoform 2B of GTPase KRas
KeywordsHYDROLASE / GTPase / Ras / KRas / KRasG13C / Nucleotide analogues / edaGDP
Function / homologysmall monomeric GTPase / Ca2+ pathway / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / edaGDP / Isoform 2B of GTPase KRas
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGoebel, L. / Mueller, M.P. / Rauh, D.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)RA 1055/5-1 Germany
German Research Foundation (DFG)GO 284/10-1 Germany
CitationJournal: Elife / Year: 2023
Title: Targeting oncogenic KRasG13C with nucleotide-based covalent inhibitors.
Authors: Goebel, L. / Kirschner, T. / Koska, S. / Rai, A. / Janning, P. / Maffini, S. / Vatheuer, H. / Czodrowski, P. / Goody, R.S. / Muller, M.P. / Rauh, D.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation
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.year
Revision 1.2Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)20,0192
Polymers19,4341
Non-polymers5851
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.400, 73.400, 54.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 19433.881 Da / Num. of mol.: 1 / Mutation: G13C
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-VJ8 / edaGDP / [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] ~{N}-[2-(propanoylamino)ethyl]carbamate


Mass: 585.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N7O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M (NH4)F, 20 % PEG3350, 67 mg/mL KRasG13C-edaGDP, 0.1 uL reservoir + 0.1 uL protein solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.6→41.243 Å / Num. obs: 22009 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.103 / Net I/σ(I): 12.71
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.966 / Num. unique obs: 3625 / CC1/2: 0.801 / Rrim(I) all: 1.016 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OBE

4obe


Resolution: 1.6→41.24 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 1101 5 %
Rwork0.158 20908 -
obs0.1601 22009 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.76 Å2 / Biso mean: 27.867 Å2 / Biso min: 13.33 Å2
Refinement stepCycle: final / Resolution: 1.6→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 38 187 1589
Biso mean--18.91 36.23 -
Num. residues----170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.670.30621360.23325782714
1.67-1.760.25271370.19925992736
1.76-1.870.23451370.181526112748
1.87-2.020.21641370.17625962733
2.02-2.220.22811370.155626122749
2.22-2.540.19211370.157326092746
2.54-3.20.22281390.161826282767
3.2-41.240.16051410.13926752816
Refinement TLS params.Method: refined / Origin x: 55.4797 Å / Origin y: 20.7789 Å / Origin z: 12.1359 Å
111213212223313233
T0.1263 Å2-0.0011 Å2-0.0027 Å2-0.1326 Å2-0.0283 Å2--0.1459 Å2
L2.1922 °20.4538 °2-0.4439 °2-1.8757 °2-0.6742 °2--1.9266 °2
S0.0014 Å °0.0861 Å °-0.1156 Å °-0.0064 Å °0.0277 Å °-0.1759 Å °0.0327 Å °0.1013 Å °-0.0385 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 169
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 187

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