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- PDB-7d5e: Left-handed G-quadruplex containing two bulges -

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Basic information

Entry
Database: PDB / ID: 7d5e
TitleLeft-handed G-quadruplex containing two bulges
Components2xBulge-LHG4motif
KeywordsDNA / G-quadruplex / Bulge / Left-handed
Function / homology: / SPERMINE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.296 Å
AuthorsDas, P. / Maity, A. / Ngo, K.H. / Winnerdy, F.R. / Bakalar, B. / Mechulam, Y. / Schmitt, E. / Phan, A.T.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2017-09 Singapore
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Bulges in left-handed G-quadruplexes.
Authors: Das, P. / Ngo, K.H. / Winnerdy, F.R. / Maity, A. / Bakalar, B. / Mechulam, Y. / Schmitt, E. / Phan, A.T.
History
DepositionSep 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2xBulge-LHG4motif
B: 2xBulge-LHG4motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,85114
Polymers17,7452
Non-polymers1,10612
Water3,747208
1
A: 2xBulge-LHG4motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3956
Polymers8,8731
Non-polymers5225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4250 Å2
MethodPISA
2
B: 2xBulge-LHG4motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4578
Polymers8,8731
Non-polymers5847
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area4220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.100, 39.810, 54.970
Angle α, β, γ (deg.)90.000, 91.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 2xBulge-LHG4motif


Mass: 8872.649 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.: 7 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.79 Å3/Da / Density % sol: 31.43 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.08 M potassium chloride, 0.04 M sodium cacodylate trihydrate pH 7.0, 60% v/v -2-methyl-2,4-pentanediol and 0.012 M spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.296→29.093 Å / Num. obs: 31051 / % possible obs: 94.67 % / Redundancy: 6 % / Biso Wilson estimate: 11.81 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.073 / Rrim(I) all: 0.18 / Net I/σ(I): 6.86
Reflection shellResolution: 1.296→1.342 Å / Rmerge(I) obs: 1.203 / Num. unique obs: 2861 / CC1/2: 0.732 / Rpim(I) all: 0.589 / Rrim(I) all: 1.345 / % possible all: 90.68

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U5M

4u5m


Resolution: 1.296→29.093 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2141 1433 4.82 %
Rwork0.1837 28288 -
obs0.1853 29721 94.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.11 Å2 / Biso mean: 17.2102 Å2 / Biso min: 8.66 Å2
Refinement stepCycle: final / Resolution: 1.296→29.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1178 64 208 1450
Biso mean--35.14 26.78 -
Num. residues----56
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071372
X-RAY DIFFRACTIONf_angle_d1.0382096
X-RAY DIFFRACTIONf_chiral_restr0.046222
X-RAY DIFFRACTIONf_plane_restr0.01256
X-RAY DIFFRACTIONf_dihedral_angle_d35.932596
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2961-1.34240.35391350.3202270791
1.3424-1.39620.33431410.2843288497
1.3962-1.45970.28631520.2636290497
1.4597-1.53660.31381230.2286291497
1.5366-1.63290.26921360.2047281996
1.6329-1.7590.21511460.1648285095
1.759-1.9360.19051560.1643283095
1.936-2.2160.2281620.1752283895
2.216-2.79160.23671320.1829279593
2.7916-29.0930.15061500.1472274790

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