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- PDB-6jjg: Crystal structure of a two-quartet DNA mixed-parallel/antiparalle... -

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Basic information

Entry
Database: PDB / ID: 6jjg
TitleCrystal structure of a two-quartet DNA mixed-parallel/antiparallel G-quadruplex
ComponentsDNA (5'-D(*GP*GP*CP*TP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3')
KeywordsDNA / G-quadruplex / two-quartet / mixed-parallel/antiparallel
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesPseudorabies virus Ea
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.969 Å
AuthorsZhang, Y.S. / Wei, D.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31672558 China
CitationJournal: To Be Published
Title: Crystal structure of a two-quartet DNA mixed-parallel/antiparallel G-quadruplex
Authors: Zhang, Y.S. / Parkinson, G.N. / Wagner, A. / Wei, D.G.
History
DepositionFeb 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,8666
Polymers8,7262
Non-polymers1404
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint0 kcal/mol
Surface area4900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.654, 46.807, 36.843
Angle α, β, γ (deg.)90.000, 110.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 4362.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pseudorabies virus Ea
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Potassium cacodylate, Potassium chloride, Sodium cacodylate, Spermine, Potassium bromide, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97907 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.969→32.672 Å / Num. obs: 5421 / % possible obs: 97.7 % / Redundancy: 6.8 % / Rpim(I) all: 0.025 / Net I/σ(I): 15.52
Reflection shellResolution: 1.969→2.08 Å / Rpim(I) all: 0.196

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JJE

6jje


Resolution: 1.969→23.075 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.29
RfactorNum. reflection% reflection
Rfree0.2743 279 5.18 %
Rwork0.2544 --
obs0.2556 5385 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166 Å2 / Biso mean: 75.888 Å2 / Biso min: 34.14 Å2
Refinement stepCycle: final / Resolution: 1.969→23.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 580 4 2 586
Biso mean--41.5 75.77 -
Num. residues----28
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9685-2.47970.34281270.31552557268498
2.4797-23.07670.26581520.24522549270196
Refinement TLS params.Method: refined / Origin x: -11.0288 Å / Origin y: -2.4043 Å / Origin z: 9.2058 Å
111213212223313233
T0.5162 Å2-0.0179 Å2-0.0244 Å2-0.4095 Å2-0.0355 Å2--0.5747 Å2
L5.3135 °21.0711 °26.7305 °2-4.5286 °20.4859 °2--10.3492 °2
S-0.5585 Å °0.3055 Å °0.8219 Å °-0.7274 Å °-0.5979 Å °0.3099 Å °-0.3251 Å °-0.0055 Å °-0.1102 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 14
2X-RAY DIFFRACTION1allB1 - 14
3X-RAY DIFFRACTION1allC1 - 3
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allS1 - 2

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