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- PDB-8fmi: Crystal structure of human KRAS at 1.12 A -

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Basic information

Entry
Database: PDB / ID: 8fmi
TitleCrystal structure of human KRAS at 1.12 A
ComponentsIsoform 2B of GTPase KRas
KeywordsHYDROLASE / cancer
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: 1.12 Å
AuthorsBrenner, R. / Landgraf, A. / Gonzalez-Gutierrez, G. / Bum-Erdene, K. / Meroueh, S.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA264471 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA197928 United States
CitationJournal: Biochemistry / Year: 2023
Title: Crystal Packing Reveals a Potential Autoinhibited KRAS Dimer Interface and a Strategy for Small-Molecule Inhibition of RAS Signaling.
Authors: Brenner, R.J. / Landgraf, A.D. / Bum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.O.
History
DepositionDec 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)19,7803
Polymers19,3131
Non-polymers4682
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.930, 39.810, 91.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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: 19312.746 Da / Num. of mol.: 1
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
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: 1.84 Å3/Da / Density % sol: 33.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium Formate 0.2 M and PEG 3350 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07216 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07216 Å / Relative weight: 1
ReflectionResolution: 1.12→36.52 Å / Num. obs: 55227 / % possible obs: 99.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 7.84 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.029 / Rrim(I) all: 0.092 / Rsym value: 0.087 / Net I/σ(I): 24.3
Reflection shellResolution: 1.12→1.14 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2494 / CC1/2: 0.735 / Rpim(I) all: 0.318 / Rrim(I) all: 0.662 / Rsym value: 0.574 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5us4

5us4


Resolution: 1.12→36.52 Å / SU ML: 0.089 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.5185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1473 2685 4.86 %
Rwork0.1195 52520 -
obs0.1209 55205 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.39 Å2
Refinement stepCycle: LAST / Resolution: 1.12→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1383 0 1 278 1662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01081467
X-RAY DIFFRACTIONf_angle_d1.23711993
X-RAY DIFFRACTIONf_chiral_restr0.0871218
X-RAY DIFFRACTIONf_plane_restr0.012261
X-RAY DIFFRACTIONf_dihedral_angle_d11.7298212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.140.29291260.25892490X-RAY DIFFRACTION90.24
1.14-1.160.20071290.17132654X-RAY DIFFRACTION96.83
1.16-1.190.1691290.13462755X-RAY DIFFRACTION99.93
1.19-1.210.17161260.12572770X-RAY DIFFRACTION99.86
1.21-1.240.17471360.1362741X-RAY DIFFRACTION99.79
1.24-1.270.18731290.13482728X-RAY DIFFRACTION99.51
1.27-1.310.17211330.12672765X-RAY DIFFRACTION99.52
1.31-1.340.18961320.11422764X-RAY DIFFRACTION99.28
1.34-1.390.12871480.10442735X-RAY DIFFRACTION99.52
1.39-1.440.13391530.09662740X-RAY DIFFRACTION100
1.44-1.490.12681650.10062754X-RAY DIFFRACTION100
1.49-1.560.13511420.09762773X-RAY DIFFRACTION100
1.56-1.640.13061460.09712776X-RAY DIFFRACTION100
1.64-1.750.13121330.10172806X-RAY DIFFRACTION100
1.75-1.880.13351370.10742792X-RAY DIFFRACTION99.97
1.88-2.070.15271410.10552813X-RAY DIFFRACTION99.93
2.07-2.370.12631760.10852796X-RAY DIFFRACTION100
2.37-2.990.14381310.12342883X-RAY DIFFRACTION100
2.99-36.520.14391730.1312985X-RAY DIFFRACTION100

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