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

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Basic information

Entry
Database: PDB / ID: 6jje
TitleCrystal structure of a two-quartet DNA mixed-parallel/antiparallel G-quadruplex (BrU)
ComponentsDNA (5'-D(*GP*GP*CP*(BRU)P*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3')
KeywordsDNA / G-quadruplex / two-quartet / mixed-parallel/antiparallel
Function / homology: / COBALT HEXAMMINE(III) / DNA / DNA (> 10)
Function and homology information
Biological speciesPseudorabies virus Ea
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.378 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 (BrU)
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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,4799
Polymers8,8552
Non-polymers6247
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-0 kcal/mol
Surface area5190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.786, 47.454, 37.782
Angle α, β, γ (deg.)90.000, 109.960, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-247-

HOH

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Components

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


Mass: 4427.686 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-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CoH18N6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 42.27 % / Description: square
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: Potassium cacodylate,Sodium cacodylate,Potassium chloride,Sodium chloride,hexammine cobalt(III) chloride,MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.91944 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91944 Å / Relative weight: 1
ReflectionResolution: 1.378→50 Å / Num. obs: 15296 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.536
Reflection shellResolution: 1.378→1.428 Å / Rmerge(I) obs: 0.289 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JJF

6jjf


Resolution: 1.378→31.49 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 24.48
RfactorNum. reflection% reflection
Rfree0.225 762 4.99 %
Rwork0.1962 --
obs0.1976 15259 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.41 Å2 / Biso mean: 19.3874 Å2 / Biso min: 6.24 Å2
Refinement stepCycle: final / Resolution: 1.378→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 580 25 95 700
Biso mean--31.5 28.93 -
Num. residues----28
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3783-1.48470.24971610.22482880304199
1.4847-1.63410.22931300.197329333063100
1.6341-1.87060.20191530.17222885303899
1.8706-2.35660.20611530.202929223075100
2.3566-35.5240.23721650.19642877304297

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