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

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Basic information

Entry
Database: PDB / ID: 6jjf
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: / COBALT HEXAMMINE(III) / DNA / DNA (> 10)
Function and homology information
Biological speciesPseudorabies virus Ea
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsZhang, Y.S. / EI Omari, K. / Duman, R. / Wagner, A. / Parkinson, G.N. / Wei, D.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31672558 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths.
Authors: Zhang, Y. / El Omari, K. / Duman, R. / Liu, S. / Haider, S. / Wagner, A. / Parkinson, G.N. / Wei, D.
History
DepositionFeb 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
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.title / _citation.year / _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
Revision 1.2Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)9,3499
Polymers8,7262
Non-polymers6247
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-5 kcal/mol
Surface area5270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.370, 47.600, 37.730
Angle α, β, γ (deg.)90.000, 110.020, 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-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


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.93 % / Description: square
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Potassium cacodylate, Sodium cacodylate, Potassium chloride, Sodium chloride, Lithium chloride, Hexammine cobalt (III) chloride, MPD

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I2311.5895
SYNCHROTRONDiamond I2323.3509
SYNCHROTRONDiamond I2331.5895
Detector
TypeIDDetectorDate
DECTRIS PILATUS 12M1PIXELMay 21, 2018
DECTRIS PILATUS 12M2PIXELJun 25, 2018
DECTRIS PILATUS 12M3PIXELJun 27, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.58951
23.35091
31
Reflection

Entry-ID: 6JJF / Redundancy: 6.4 %

Resolution (Å)Num. obs% possible obs (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.47-23.8127049825.090.9980.036117.7
2.19-35.34386598.60.9990.076236.7
1.4-35.371488099.710.064326.8
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.47-1.520.5131.111220.644186.6
2.19-2.260.16311.42860.975286.4
1.4-1.422.179114800.6683

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→23.8 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 610 4.81 %
Rwork0.1921 12073 -
obs0.1924 12683 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.76 Å2 / Biso mean: 33.7619 Å2 / Biso min: 19.85 Å2
Refinement stepCycle: final / Resolution: 1.47→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 580 25 67 672
Biso mean--50.68 39.21 -
Num. residues----28
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.47-1.61790.34711210.2829291794
1.6179-1.8520.25911560.2065302399
1.852-2.3330.22181790.21473043100
2.333-23.80.17361540.1772309099
Refinement TLS params.Method: refined / Origin x: -3.603 Å / Origin y: -7.6468 Å / Origin z: -7.6421 Å
111213212223313233
T0.2338 Å2-0.0152 Å2-0.0058 Å2-0.2214 Å2-0.0077 Å2--0.2398 Å2
L1.7307 °2-0.6688 °2-0.6631 °2-1.4693 °2-0.101 °2--2.0666 °2
S-0.0404 Å °0.1328 Å °-0.1068 Å °-0.0897 Å °0.0395 Å °0.0078 Å °-0.0505 Å °0.048 Å °-0.0005 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 DIFFRACTION1allE101 - 103
6X-RAY DIFFRACTION1allS1 - 68

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