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- PDB-6n65: KRAS G-quadruplex G16T mutant. -

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Basic information

Entry
Database: PDB / ID: 6n65
TitleKRAS G-quadruplex G16T mutant.
ComponentsKRAS G-quadruplex G16T mutant
KeywordsDNA / KRAS / G-quadruplex / promoter sequence / G16T mutant
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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
DepositionNov 25, 2018Deposition 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 11, 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_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.pdbx_dist_value / _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_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: KRAS G-quadruplex G16T mutant
B: KRAS G-quadruplex G16T mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1697
Polymers13,9732
Non-polymers1955
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: It is unclear if this represents the solution oligomeric state of the quadruplex.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.693, 30.127, 52.970
Angle α, β, γ (deg.)90.000, 94.510, 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 KRAS G-quadruplex G16T mutant


Mass: 6986.514 Da / Num. of mol.: 2 / Mutation: G16T / 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.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.08 M sodium chloride, 0.012 M potassium chloride, 0.02 magnesium chloride hexahydrate, 0.04 M sodium cacodylate trihydrate pH 7.0, 35% MPD, 0.012 M spermine tetrahydrochloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.6→30.13 Å / Num. obs: 13756 / % possible obs: 96.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.024 / Rrim(I) all: 0.059 / Net I/σ(I): 16 / Num. measured all: 86330 / Scaling rejects: 1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.31 / Num. unique obs: 501 / CC1/2: 0.976 / Rpim(I) all: 0.156 / Rrim(I) all: 0.349 / % possible all: 74.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I2V

5i2v


Resolution: 1.6→29.409 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.07
RfactorNum. reflection% reflection
Rfree0.2407 684 4.99 %
Rwork0.2101 --
obs0.2115 13707 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.76 Å2 / Biso mean: 29.0368 Å2 / Biso min: 13.35 Å2
Refinement stepCycle: final / Resolution: 1.6→29.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 932 5 64 1001
Biso mean--15.62 32.74 -
Num. residues----44
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A394X-RAY DIFFRACTION0.916TORSIONAL
12B394X-RAY DIFFRACTION0.916TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.72350.26191210.22692207232883
1.7235-1.89690.26581570.209526762833100
1.8969-2.17140.27321420.233526932835100
2.1714-2.73540.26451260.240727012827100
2.7354-29.41350.2161380.18972746288498

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