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- PDB-6mc3: Crystal structure of a tetrameric DNA fold-back quadruplex -

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Basic information

Entry
Database: PDB / ID: 6mc3
TitleCrystal structure of a tetrameric DNA fold-back quadruplex
ComponentsDNA (5'-D(*CP*GP*TP*GP*AP*GP*GP*CP*G)-3')
KeywordsDNA / quadruplex / fold-back / hexad / non-canonical
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsChu, B. / Paukstelis, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1149665 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Crystal Structure of a Tetrameric DNA Fold-Back Quadruplex.
Authors: Chu, B. / Zhang, D. / Hwang, W. / Paukstelis, P.J.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,33310
Polymers11,1874
Non-polymers1466
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-31 kcal/mol
Surface area5120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.135, 46.430, 71.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-122-

HOH

21B-125-

HOH

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Components

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


Mass: 2796.835 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 15% PEG400, 120 mM magnesium chloride, 30 mM sodium cacodylate, equilibrated against 20% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.57→28.42 Å / Num. obs: 16520 / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.036 / Net I/σ(I): 8.3
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 3.668 / Num. unique obs: 802 / Rpim(I) all: 1.531

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→28.42 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 10.313 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24344 793 4.8 %RANDOM
Rwork0.20042 ---
obs0.20272 15701 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.605 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å2-0 Å2-0 Å2
2---1.22 Å20 Å2
3---2.99 Å2
Refinement stepCycle: 1 / Resolution: 1.57→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 744 6 110 860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.011898
X-RAY DIFFRACTIONr_bond_other_d0.0060.02431
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.1451392
X-RAY DIFFRACTIONr_angle_other_deg1.96831019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02480
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02204
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.6223.793897
X-RAY DIFFRACTIONr_scbond_other6.6223.793896
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4665.6991392
X-RAY DIFFRACTIONr_long_range_B_refined8.32235.7721421
X-RAY DIFFRACTIONr_long_range_B_other7.78634.8121377
X-RAY DIFFRACTIONr_rigid_bond_restr6.00331328
X-RAY DIFFRACTIONr_sphericity_free34.314547
X-RAY DIFFRACTIONr_sphericity_bonded22.4151296
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 61 -
Rwork0.388 1133 -
obs--99.17 %

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