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- PDB-6tzr: A DNA G-quadruplex/i-motif hybrid -

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Basic information

Entry
Database: PDB / ID: 6tzr
TitleA DNA G-quadruplex/i-motif hybrid
ComponentsDNA (5'-D(*CP*CP*AP*GP*GP*CP*(BRU)P*GP*CP*AP*A)-3')
KeywordsDNA / G-quadruplex / i-motif / quadruplex / hybrid / non-duplex / noncanonical
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsChu, B. / Paukstelis, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1149665 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: A DNA G-quadruplex/i-motif hybrid.
Authors: Chu, B. / Zhang, D. / Paukstelis, P.J.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
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.year / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,9533
Polymers6,8162
Non-polymers1371
Water00
1
A: DNA (5'-D(*CP*CP*AP*GP*GP*CP*(BRU)P*GP*CP*AP*A)-3')
B: DNA (5'-D(*CP*CP*AP*GP*GP*CP*(BRU)P*GP*CP*AP*A)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)13,9076
Polymers13,6324
Non-polymers2752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)37.099, 37.099, 98.309
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-101-

BA

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Components

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


Mass: 3408.070 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.: 1 / Source method: obtained synthetically / Formula: Ba
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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% PEG 400, 40 mM barium chloride, 10 mM spermidine, 30 mM Bis-Tris pH 8.5; Equilibrated against 5% PEG 400 and 3 ul of glacial acetic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9196 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 2.4→32.77 Å / Num. obs: 3399 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.032 / Rrim(I) all: 0.09 / Net I/σ(I): 11 / Num. measured all: 30095
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.865 / Num. measured all: 3381 / Num. unique obs: 358 / CC1/2: 0.984 / Rpim(I) all: 0.298 / Rrim(I) all: 0.917 / Net I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→30.56 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.945 / SU B: 12.827 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.257
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 367 10.9 %RANDOM
Rwork0.2121 ---
obs0.2178 3010 99.82 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 122.26 Å2 / Biso mean: 73.861 Å2 / Biso min: 48.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å2-0 Å2
2---0.14 Å20 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 2.4→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 444 1 0 445
Biso mean--64.92 --
Num. residues----22
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.011498
X-RAY DIFFRACTIONr_bond_other_d0.0020.02240
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.303764
X-RAY DIFFRACTIONr_angle_other_deg1.6863568
X-RAY DIFFRACTIONr_chiral_restr0.1140.266
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02124
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.605 21 -
Rwork0.589 229 -
all-250 -
obs--100 %

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