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- PDB-6n4g: Crystal structure of a tetrameric DNA fold-back quadruplex -

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Basic information

Entry
Database: PDB / ID: 6n4g
TitleCrystal structure of a tetrameric DNA fold-back quadruplex
ComponentsDNA (5'-D(*CP*GP*TP*TP*AP*GP*GP*CP*G)-3')
KeywordsDNA / quadruplex / fold-back / hexad / non-canonical
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionNov 19, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionDec 5, 2018ID: 6MC5
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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_alt_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,78011
Polymers5,5442
Non-polymers1,2369
Water2,450136
1
A: DNA (5'-D(*CP*GP*TP*TP*AP*GP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*TP*AP*GP*GP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)13,55922
Polymers11,0874
Non-polymers2,47218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area5920 Å2
ΔGint-82 kcal/mol
Surface area5410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.329, 53.705, 34.233
Angle α, β, γ (deg.)90.00, 102.04, 90.00
Int Tables number5
Space group name H-MI121

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Components

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


Mass: 2771.822 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 15% MPD, 120 mM barium chloride, 30 mM sodium cacodylate, equilibrated against 20% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
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: 1.4→28.41 Å / Num. obs: 9187 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.052 / Net I/σ(I): 8.1
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.336 / Num. unique obs: 452 / Rpim(I) all: 0.224

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→28.41 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.388 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21915 433 4.7 %RANDOM
Rwork0.1469 ---
obs0.15053 8753 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.634 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å2-0 Å20.24 Å2
2---2.09 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.4→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 368 9 136 513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.011412
X-RAY DIFFRACTIONr_bond_other_d0.0030.02204
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.151634
X-RAY DIFFRACTIONr_angle_other_deg1.8223482
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_restr0.0790.254
X-RAY DIFFRACTIONr_gen_planes_refined0.0340.02218
X-RAY DIFFRACTIONr_gen_planes_other0.0060.0288
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_it2.4371.641412
X-RAY DIFFRACTIONr_scbond_other2.4391.641411
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8852.476635
X-RAY DIFFRACTIONr_long_range_B_refined4.59818.346685
X-RAY DIFFRACTIONr_long_range_B_other3.8216.611634
X-RAY DIFFRACTIONr_rigid_bond_restr4.2473616
X-RAY DIFFRACTIONr_sphericity_free19.886572
X-RAY DIFFRACTIONr_sphericity_bonded9.4475649
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 34 -
Rwork0.198 645 -
obs--98.12 %

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