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- PDB-8taa: Right-left hybrid parallel G-quadruplex in complex with N-methyl ... -

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Basic information

Entry
Database: PDB / ID: 8taa
TitleRight-left hybrid parallel G-quadruplex in complex with N-methyl mesoporphyrin
ComponentsDNA (25-MER)
KeywordsDNA / G-quadruplex / right-left-handed / parallel / NMM
Function / homology: / N-METHYLMESOPORPHYRIN / SPERMINE (FULLY PROTONATED FORM) / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeth, P.C. / Yatsunyk, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Interaction of N-methylmesoporphyrin IX with a hybrid left-/right-handed G-quadruplex motif from the promoter of the SLC2A1 gene.
Authors: Seth, P. / Xing, E. / Hendrickson, A.D. / Li, K. / Monsen, R. / Chaires, J.B. / Neidle, S. / Yatsunyk, L.A.
History
DepositionJun 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 2.0Oct 16, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Experimental preparation / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / chem_comp_atom / chem_comp_bond / entity / exptl_crystal_grow / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _exptl_crystal_grow.pdbx_details / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_entry_details.has_protein_modification / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work
Description: Model completeness
Details: Added more atoms to the ligand and additional waters. Split four nucleotides due to two different positions for the phosphate backbones.
Provider: author / Type: Coordinate replacement
Revision 2.1Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9927
Polymers7,9691
Non-polymers1,0236
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.897, 30.897, 141.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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DNA chain , 1 types, 1 molecules A

#1: DNA chain DNA (25-MER)


Mass: 7969.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 68 molecules

#2: Chemical ChemComp-SPK / SPERMINE (FULLY PROTONATED FORM)


Mass: 206.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H30N4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40N4O4
#5: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43 % / Description: Amorphous cubes
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2 mM Spermine, 45% MPD, 0.08 M NaCl, 0.04 M NaCaCo pH 6.0

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.45→141.54 Å / Num. obs: 13141 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 28.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.015 / Rrim(I) all: 0.051 / Net I/σ(I): 21
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 1.789 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 647 / CC1/2: 0.678 / Rpim(I) all: 0.523 / Rrim(I) all: 1.866 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Coot0.8.9.2model building
PHENIX1.21.2_5419phasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→35.39 Å / SU ML: 0.1904 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.3357
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 702 5.38 %RANDOM
Rwork0.1783 12347 --
obs0.1809 13049 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.75 Å2
Refinement stepCycle: LAST / Resolution: 1.45→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 530 61 62 653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063752
X-RAY DIFFRACTIONf_angle_d1.00931162
X-RAY DIFFRACTIONf_chiral_restr0.041116
X-RAY DIFFRACTIONf_plane_restr0.010433
X-RAY DIFFRACTIONf_dihedral_angle_d34.9078331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.560.30811420.23872400X-RAY DIFFRACTION100
1.56-1.720.22831270.17892414X-RAY DIFFRACTION99.73
1.72-1.970.29371370.18932408X-RAY DIFFRACTION99.84
1.97-2.480.26491420.23682471X-RAY DIFFRACTION100
2.48-35.390.20461540.16082654X-RAY DIFFRACTION99.79

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