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- PDB-4u5m: Structure of a left-handed DNA G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 4u5m
TitleStructure of a left-handed DNA G-quadruplex
ComponentsDNA (28-MER)
KeywordsDNA / quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSchmitt, E. / Mechulam, Y. / Phan, A.T. / Brahim, H. / Chung, W.J. / Lim, K.W.
Funding support Singapore, France, 4items
OrganizationGrant numberCountry
Ministry of education Singapore
Nanyang technological university Singapore
Centre National de la Recherche ScientifiqueUMR7654 France
Ecole polytechniqueUMR7654 France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of a left-handed DNA G-quadruplex.
Authors: Chung, W.J. / Heddi, B. / Schmitt, E. / Lim, K.W. / Mechulam, Y. / Phan, A.T.
History
DepositionJul 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0536
Polymers8,8731
Non-polymers1815
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-8 kcal/mol
Surface area4330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.886, 51.886, 40.167
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-235-

HOH

21A-237-

HOH

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Components

#1: DNA chain DNA (28-MER)


Mass: 8872.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.76 Å3/Da / Density % sol: 30.08 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: methyl pentane diol, cacodylate, KCl, Mg

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→45 Å / Num. all: 9887 / Num. obs: 9887 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 12.3 Å2 / Rsym value: 0.083 / Net I/σ(I): 18.5
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.76 / % possible all: 77.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSNov, 2013data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→44.935 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.18 478 4.84 %Random
Rwork0.141 ---
obs0.1429 9875 95.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 589 5 94 688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008709
X-RAY DIFFRACTIONf_angle_d1.091105
X-RAY DIFFRACTIONf_dihedral_angle_d38.186302
X-RAY DIFFRACTIONf_chiral_restr0.048119
X-RAY DIFFRACTIONf_plane_restr0.01430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4997-1.71670.2671410.15332806X-RAY DIFFRACTION87
1.7167-2.16290.20671800.14783229X-RAY DIFFRACTION100
2.1629-44.95480.15161570.13553362X-RAY DIFFRACTION100

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