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- PDB-6wck: KRAS G-quadruplex G16T mutant with Bromo Uracil replacing T8 and T16. -

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Basic information

Entry
Database: PDB / ID: 6wck
TitleKRAS G-quadruplex G16T mutant with Bromo Uracil replacing T8 and T16.
ComponentsDNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*(BRU)P*GP*TP*GP*GP*GP*AP*AP*(BRU)P*AP*GP*GP*GP*AP*A)-3')
KeywordsDNA / KRAS / G-quadruplex / promoter sequence / G16T mutant / Bromouracil
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.801 Å
AuthorsSchmidberger, J.W. / Ou, A. / Smith, N.M. / Iyer, K.S. / Bond, C.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1139936 Australia
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A pi-stacking interactions for small-molecule recognition.
Authors: Ou, A. / Schmidberger, J.W. / Wilson, K.A. / Evans, C.W. / Hargreaves, J.A. / Grigg, M. / O'Mara, M.L. / Iyer, K.S. / Bond, C.S. / Smith, N.M.
History
DepositionMar 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*(BRU)P*GP*TP*GP*GP*GP*AP*AP*(BRU)P*AP*GP*GP*GP*AP*A)-3')
B: DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*(BRU)P*GP*TP*GP*GP*GP*AP*AP*(BRU)P*AP*GP*GP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4287
Polymers14,2332
Non-polymers1955
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.452, 29.943, 52.691
Angle α, β, γ (deg.)90.000, 94.620, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 3 through 22)
21(chain B and resid 3 through 22)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DA / End label comp-ID: DA / Auth seq-ID: 3 - 22 / Label seq-ID: 3 - 22

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 3 through 22)AA
2(chain B and resid 3 through 22)BB

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Components

#1: DNA chain DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*(BRU)P*GP*TP*GP*GP*GP*AP*AP*(BRU)P*AP*GP*GP*GP*AP*A)-3')


Mass: 7116.254 Da / Num. of mol.: 2 / Mutation: T8BrU, G16BrU / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.85 Å3/Da / Density % sol: 33.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 80 mM NaCl, 12 mM KCl, 20 mM MgCl.6H2O, 40 mM Na-cacodylate.3H2O pH 7.0, 35% v/v MPD, 12 mM spermine.4HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9199 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 1.8→33.343 Å / Num. obs: 9608 / % possible obs: 97.7 % / Redundancy: 7 % / Biso Wilson estimate: 21.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.047 / Rrim(I) all: 0.126 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.845.11.12422984480.5530.5311.2481.380.2
9-33.346.10.051557910.9990.0220.05637.498

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
MOLREPphasing
PHENIX1.9refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i2v

5i2v


Resolution: 1.801→33.343 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.03
RfactorNum. reflection% reflection
Rfree0.2414 471 4.93 %
Rwork0.1967 --
obs0.1988 9561 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.1 Å2 / Biso mean: 29.2003 Å2 / Biso min: 8.84 Å2
Refinement stepCycle: final / Resolution: 1.801→33.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 932 5 92 1029
Biso mean--12.65 31.84 -
Num. residues----44
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A370X-RAY DIFFRACTION0.668TORSIONAL
12B370X-RAY DIFFRACTION0.668TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.801-2.06140.29951690.2354280692
2.0614-2.5970.2521450.22883128100
2.597-33.3430.22181570.174315699

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