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- PDB-8rmh: Crystal structure of parallel G-quadruplex containing T-tetrads a... -

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Basic information

Entry
Database: PDB / ID: 8rmh
TitleCrystal structure of parallel G-quadruplex containing T-tetrads and TG-octaplet
ComponentsDNA (5'-D(*TP*GP*GP*TP*GP*GP*T)-3')
KeywordsDNA / Quadruplex / T-tetrad / Octaplet / Parallel
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsAbdullrahman, A. / El Omari, K. / Paterson, N. / Orr, C. / Lambert, M. / Cardin, C.J. / Sanchez-Weatherby, J. / Hall, J.P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionH2020-MSCA-INT-2019-861European Union
CitationJournal: To Be Published
Title: Crystal structure of parallel G-quadruplex containing T-tetrads and TG-octaplet
Authors: Abdullrahman, A. / El Omari, K. / Paterson, N. / Orr, C. / Lambert, M. / Sandy, J. / Mikolajek, H. / Cardin, C.J. / Sanchez-Weatherby, J. / Hall, J.P.
History
DepositionJan 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*GP*GP*TP*GP*GP*T)-3')
B: DNA (5'-D(*TP*GP*GP*TP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,86916
Polymers4,3692
Non-polymers50014
Water1,08160
1
A: DNA (5'-D(*TP*GP*GP*TP*GP*GP*T)-3')
B: DNA (5'-D(*TP*GP*GP*TP*GP*GP*T)-3')
hetero molecules

A: DNA (5'-D(*TP*GP*GP*TP*GP*GP*T)-3')
B: DNA (5'-D(*TP*GP*GP*TP*GP*GP*T)-3')
hetero molecules

A: DNA (5'-D(*TP*GP*GP*TP*GP*GP*T)-3')
B: DNA (5'-D(*TP*GP*GP*TP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,60848
Polymers13,1076
Non-polymers1,50142
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
Unit cell
Length a, b, c (Å)40.436, 40.436, 40.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-101-

K

21A-102-

K

31A-103-

K

41A-104-

K

51A-105-

K

61A-106-

K

71A-107-

K

81A-108-

MG

91A-109-

NA

101A-110-

NA

111B-101-

K

121B-102-

K

131B-103-

K

141A-216-

HOH

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Components

#1: DNA chain DNA (5'-D(*TP*GP*GP*TP*GP*GP*T)-3')


Mass: 2184.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.89 Å3/Da / Density % sol: 35.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: A solution containing DNA 1.8 mM, 0.02 M Sodium Cacodylate pH 5.5, 0.1 M NaCl, 0.01 mM MgCl2 was mixed 1:1 with a solution containing 0.2 M Potassium chloride, 0.05 M Sodium cacodylate ...Details: A solution containing DNA 1.8 mM, 0.02 M Sodium Cacodylate pH 5.5, 0.1 M NaCl, 0.01 mM MgCl2 was mixed 1:1 with a solution containing 0.2 M Potassium chloride, 0.05 M Sodium cacodylate trihydrate pH 5.9, 10% w/v Polyethylene glycol 4000 & 0.01 M Magnesium chloride hexahydrate.

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 1.1271 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Sep 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.15→40.48 Å / Num. obs: 12480 / % possible obs: 100 % / Redundancy: 126.9 % / Biso Wilson estimate: 10.52 Å2 / CC1/2: 1 / Net I/σ(I): 0.353
Reflection shellResolution: 1.15→1.17 Å / Num. unique obs: 589 / CC1/2: 0.567

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
XSCALEdata scaling
ACORNphasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→40.48 Å / SU ML: 0.1731 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.032
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.19 1216 5.4 %
Rwork0.1514 21323 -
obs0.1536 12352 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.33 Å2
Refinement stepCycle: LAST / Resolution: 1.15→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 290 14 60 364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112324
X-RAY DIFFRACTIONf_angle_d1.2766500
X-RAY DIFFRACTIONf_chiral_restr0.052254
X-RAY DIFFRACTIONf_plane_restr0.016414
X-RAY DIFFRACTIONf_dihedral_angle_d33.3676132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.20.33021090.33732212X-RAY DIFFRACTION91.96
1.2-1.250.371310.30272390X-RAY DIFFRACTION99.41
1.25-1.320.33771200.26522412X-RAY DIFFRACTION99.92
1.32-1.40.2741080.21242430X-RAY DIFFRACTION100
1.4-1.510.21471360.17912403X-RAY DIFFRACTION99.69
1.51-1.660.19661730.14742303X-RAY DIFFRACTION99.84
1.66-1.90.1451530.12372390X-RAY DIFFRACTION99.53
1.9-2.390.15971310.11452412X-RAY DIFFRACTION100
2.39-40.480.15761550.10772371X-RAY DIFFRACTION99.21

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