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- PDB-8dhc: Crystal structure of an i-motif from the HRAS promoter region -

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Basic information

Entry
Database: PDB / ID: 8dhc
TitleCrystal structure of an i-motif from the HRAS promoter region
ComponentsHRAS DNA
KeywordsDNA / HRAS / i-Motif / oncogene
Function / homology1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsYatsunyk, L.A. / Li, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Crystal Structure of an i-Motif from the HRAS Oncogene Promoter.
Authors: Li, K.S. / Jordan, D. / Lin, L.Y. / McCarthy, S.E. / Schneekloth Jr., J.S. / Yatsunyk, L.A.
History
DepositionJun 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 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: HRAS DNA
B: HRAS DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4693
Polymers16,2902
Non-polymers1781
Water1267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, There are bands for both monomer and a dimer on the native gel.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.126, 29.656, 54.326
Angle α, β, γ (deg.)90.000, 93.100, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: DNA chain HRAS DNA


Mass: 8145.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.85 Å3/Da / Density % sol: 56.9 % / Description: rectangular prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.001 M Spermine Tetrahydrochloride, 0.05 M MES pH 6.5, 17% w/v PEG 4K

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.02→59.48 Å / Num. obs: 12489 / % possible obs: 97.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 53.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.027 / Rrim(I) all: 0.054 / Net I/σ(I): 10.6
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.391 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 817 / CC1/2: 0.765 / Rpim(I) all: 0.85 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8CXF

8cxf


Resolution: 2.02→59.48 Å / SU ML: 0.3906 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 46.8033
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.254 628 5.11 %
Rwork0.252 11668 -
obs0.2522 12296 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.1 Å2
Refinement stepCycle: LAST / Resolution: 2.02→59.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1042 12 7 1061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01051173
X-RAY DIFFRACTIONf_angle_d1.2281796
X-RAY DIFFRACTIONf_chiral_restr0.0552208
X-RAY DIFFRACTIONf_plane_restr0.008152
X-RAY DIFFRACTIONf_dihedral_angle_d33.5457520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.230.5641690.4812832X-RAY DIFFRACTION95.76
2.23-2.550.45171560.37892934X-RAY DIFFRACTION97.66
2.55-3.210.40241630.32832910X-RAY DIFFRACTION96.64
3.21-59.480.18011400.19992992X-RAY DIFFRACTION95.96

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