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- PDB-7lz5: Crystal structure of oncogenic KRAS Q61E GMPPCP-bound -

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Basic information

Entry
Database: PDB / ID: 7lz5
TitleCrystal structure of oncogenic KRAS Q61E GMPPCP-bound
ComponentsIsoform 2B of GTPase KRas
KeywordsONCOPROTEIN / oncogenic / active state
Function / homologysmall monomeric GTPase / Ca2+ pathway / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Isoform 2B of GTPase KRas
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCarey, L.M. / Campbell, S.L.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)
CitationJournal: To Be Published
Title: Crystal structure of oncogenic KRAS Q61E GMPPCP-bound
Authors: Huynh, M.
History
DepositionMar 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8023
Polymers19,2571
Non-polymers5462
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.413, 94.413, 119.326
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-25-

GLN

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Components

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


Mass: 19256.678 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 (E. coli) / References: UniProt: P01116-2, small monomeric GTPase
#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, 0.2 M ammonium sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→38.7 Å / Num. obs: 32859 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 12.79 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 38.1
Reflection shellResolution: 1.5→1.538 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.28 / Num. unique obs: 1624 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VQ2

5vq2


Resolution: 1.5→38.68 Å / SU ML: 0.1016 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.5277 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1791 1990 6.06 %
Rwork0.1639 30849 -
obs0.1648 32839 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 33 131 1495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01471487
X-RAY DIFFRACTIONf_angle_d1.27352032
X-RAY DIFFRACTIONf_chiral_restr0.0804223
X-RAY DIFFRACTIONf_plane_restr0.0081266
X-RAY DIFFRACTIONf_dihedral_angle_d27.9303563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.18081380.17262141X-RAY DIFFRACTION98.15
1.54-1.580.21241360.1592176X-RAY DIFFRACTION100
1.58-1.630.17871410.16032182X-RAY DIFFRACTION100
1.63-1.680.19121360.1642210X-RAY DIFFRACTION100
1.68-1.740.16111440.16072171X-RAY DIFFRACTION100
1.74-1.810.17831400.15732194X-RAY DIFFRACTION100
1.81-1.890.17131490.15572210X-RAY DIFFRACTION100
1.89-1.990.17441320.14892188X-RAY DIFFRACTION100
1.99-2.110.171470.15752201X-RAY DIFFRACTION100
2.11-2.280.16261390.15522203X-RAY DIFFRACTION100
2.28-2.510.15981480.15792218X-RAY DIFFRACTION100
2.51-2.870.16991420.16942215X-RAY DIFFRACTION100
2.87-3.610.1851400.16662240X-RAY DIFFRACTION99.96
3.61-38.680.1991580.17632300X-RAY DIFFRACTION99.35

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