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- PDB-6kfl: Crystal structure of a two-quartet DNA G-quadruplex complexed wit... -

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Basic information

Entry
Database: PDB / ID: 6kfl
TitleCrystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin TMPyP4
ComponentsDNA (5'-D(*GP*GP*CP*TP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3')
KeywordsDNA / G-quadruplex / two-quartet / complex
Function / homology: / COBALT HEXAMMINE(III) / Chem-POH / DNA / DNA (> 10)
Function and homology information
Biological speciesPseudorabies virus Ea
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsZhang, Y.S. / Parkinson, G.N. / 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 G-quadruplex complexed with the porphyrin TMPyP4
Authors: Zhang, Y.S. / Parkinson, G.N. / Wei, D.G.
History
DepositionJul 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 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)9,7228
Polymers8,7262
Non-polymers9966
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-1 kcal/mol
Surface area4610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.152, 47.192, 38.133
Angle α, β, γ (deg.)90.000, 113.150, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-105-

POH

21B-106-

HOH

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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: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudorabies virus Ea / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POH / (1Z,4Z,9Z,15Z)-5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)-21,23-dihydroporphyrin / TMPyP4


Mass: 678.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H38N8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: KCaco,Nacaco,KCl,NaCl,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: 1.03923 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03923 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 5961 / % possible obs: 96.22 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.81
Reflection shellResolution: 1.92→1.989 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.354 / Num. unique obs: 487

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JJF

6jjf


Resolution: 1.92→35.063 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.06
RfactorNum. reflection% reflection
Rfree0.2617 331 5.65 %
Rwork0.2181 --
obs0.2207 5854 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.96 Å2 / Biso mean: 34.7276 Å2 / Biso min: 7.38 Å2
Refinement stepCycle: final / Resolution: 1.92→35.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 580 63 54 697
Biso mean--55.04 34.27 -
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 (%)
1.9197-2.41860.30241630.2232685284894
2.4186-35.06910.24681680.21612838300699
Refinement TLS params.Method: refined / Origin x: 12.5944 Å / Origin y: -7.8122 Å / Origin z: 9.663 Å
111213212223313233
T0.1625 Å20.0239 Å2-0.0135 Å2-0.1842 Å2-0.001 Å2--0.1162 Å2
L2.0864 °20.022 °20.2574 °2-2.9184 °2-0.4268 °2--1.9253 °2
S-0.0371 Å °0.6077 Å °0.077 Å °-0.4864 Å °-0.0778 Å °0.1598 Å °-0.0011 Å °-0.0803 Å °0.0469 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 14
2X-RAY DIFFRACTION1allB1 - 14
3X-RAY DIFFRACTION1allC1 - 4
4X-RAY DIFFRACTION1allP102
5X-RAY DIFFRACTION1allE101
6X-RAY DIFFRACTION1allS1 - 56

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