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- PDB-5xk0: Structure of 8-mer DNA2 -

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Basic information

Entry
Database: PDB / ID: 5xk0
TitleStructure of 8-mer DNA2
ComponentsDNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')
KeywordsDNA / duplex
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.451 Å
AuthorsLiu, H.H. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370728 China
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: A DNA Structure Containing AgI -Mediated G:G and C:C Base Pairs
Authors: Liu, H.H. / Shen, F.S. / Haruehanroengra, P. / Yao, Q.Q. / Cheng, Y.S. / Chen, Y.Q. / Yang, C. / Zhang, J. / Wu, B.X. / Luo, Q. / Cui, R.X. / Li, J.X. / Ma, J.B. / Sheng, J. / Gan, J.H.
History
DepositionMay 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4131
Polymers2,4131
Non-polymers00
Water64936
1
A: DNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')

A: DNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8252
Polymers4,8252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area760 Å2
ΔGint-5 kcal/mol
Surface area3080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.012, 42.012, 25.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')


Mass: 2412.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.23 % / Description: diamond
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% v/v MPD, 40mM Sodium cacodylate pH 6.0, 12mM Spermine tetra-HCl, 80mM KCl, 20mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 4199 / % possible obs: 98.6 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 82.3
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 12.9 / Num. unique obs: 358 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5WSP

5wsp


Resolution: 1.451→29.707 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 18.6
RfactorNum. reflection% reflection
Rfree0.1956 190 4.52 %
Rwork0.1803 --
obs0.181 4199 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.451→29.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 160 0 36 196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006179
X-RAY DIFFRACTIONf_angle_d0.919274
X-RAY DIFFRACTIONf_dihedral_angle_d14.5676
X-RAY DIFFRACTIONf_chiral_restr0.04131
X-RAY DIFFRACTIONf_plane_restr0.0098
LS refinement shellResolution: 1.4513→1.5 Å
RfactorNum. reflection% reflection
Rfree0.1956 190 -
Rwork0.1823 345 -
obs--98 %
Refinement TLS params.Method: refined / Origin x: 9.5067 Å / Origin y: 9.0897 Å / Origin z: 2.4899 Å
111213212223313233
T0.223 Å20.001 Å20.0392 Å2-0.1966 Å20.0085 Å2--0.1895 Å2
L1.7947 °2-1.927 °2-0.0487 °2-6.1765 °22.0046 °2--2.133 °2
S-0.1305 Å °-0.1571 Å °0.0532 Å °0.6226 Å °0.195 Å °-0.0137 Å °0.0978 Å °-0.0281 Å °-0.059 Å °
Refinement TLS groupSelection details: all

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