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- PDB-7d5d: Left-handed G-quadruplex containing one bulge -

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Basic information

Entry
Database: PDB / ID: 7d5d
TitleLeft-handed G-quadruplex containing one bulge
Components1xBulge-LHG4motif
KeywordsDNA / Left-handed / G-quadruplex / Bulge / Z-G4
Function / homology: / SPERMINE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsDas, P. / Ngo, K.H. / Winnerdy, F.R. / Maity, A. / 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: 1xBulge-LHG4motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0906
Polymers8,5681
Non-polymers5225
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint1 kcal/mol
Surface area4250 Å2
Unit cell
Length a, b, c (Å)29.215, 40.037, 30.376
Angle α, β, γ (deg.)90.000, 115.870, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: DNA chain 1xBulge-LHG4motif


Mass: 8568.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.87 Å3/Da / Density % sol: 34.07 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.04 M sodium cacodylate trihydrate pH 6.0, 55% 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 2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.18→27.33 Å / Num. obs: 20747 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 8.52 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.052 / Rrim(I) all: 0.135 / Net I/σ(I): 9
Reflection shellResolution: 1.182→1.224 Å / Rmerge(I) obs: 0.938 / Num. unique obs: 2060 / CC1/2: 0.5 / Rpim(I) all: 0.415 / Rrim(I) all: 1.028

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U5M
Resolution: 1.18→27.33 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.724 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1679 921 4.4 %RANDOM
Rwork0.1191 ---
obs0.1212 19779 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.28 Å2 / Biso mean: 14.786 Å2 / Biso min: 5.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.3 Å2
2---0.58 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: final / Resolution: 1.18→27.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 569 59 158 786
Biso mean--21.13 33.27 -
Num. residues----27
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.011690
X-RAY DIFFRACTIONr_bond_other_d0.0080.02413
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.2351038
X-RAY DIFFRACTIONr_angle_other_deg2.0813976
X-RAY DIFFRACTIONr_chiral_restr0.1080.281
X-RAY DIFFRACTIONr_gen_planes_refined0.0410.02332
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02116
X-RAY DIFFRACTIONr_rigid_bond_restr5.18131103
X-RAY DIFFRACTIONr_sphericity_free34.543593
X-RAY DIFFRACTIONr_sphericity_bonded12.32551106
LS refinement shellResolution: 1.182→1.212 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 72 -
Rwork0.18 1468 -
all-1540 -
obs--100 %

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