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- PDB-5xk1: Structure of 8-mer DNA3 -

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Basic information

Entry
Database: PDB / ID: 5xk1
TitleStructure of 8-mer DNA3
ComponentsDNA (5'-D(*GP*GP*AP*GP*CP*CP*CP*C)-3')
KeywordsDNA / duplex
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 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*GP*AP*GP*CP*CP*CP*C)-3')
C: DNA (5'-D(*GP*GP*AP*GP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8252
Polymers4,8252
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-5 kcal/mol
Surface area3060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.595, 44.595, 41.865
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


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


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.49 Å3/Da / Density % sol: 50.61 % / Description: rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% v/v MPD, 40mM Sodium cacodylate pH 7.0, 12mM Spermine tetra-HCl, 80mM NaCl

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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: 1.5→30 Å / Num. obs: 7613 / % possible obs: 100 % / Redundancy: 18.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 18
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4 / Num. unique obs: 770 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F4N

4f4n


Resolution: 1.501→28.387 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.46
RfactorNum. reflection% reflection
Rfree0.196 406 5.33 %
Rwork0.162 --
obs0.1638 7613 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.501→28.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 320 0 41 361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007358
X-RAY DIFFRACTIONf_angle_d0.838548
X-RAY DIFFRACTIONf_dihedral_angle_d12.244152
X-RAY DIFFRACTIONf_chiral_restr0.03562
X-RAY DIFFRACTIONf_plane_restr0.00816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5008-1.7180.2191090.16352389X-RAY DIFFRACTION98
1.718-2.16430.17511550.1752386X-RAY DIFFRACTION100
2.1643-28.39170.20361420.15592432X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.5561 Å / Origin y: 16.7512 Å / Origin z: 0.866 Å
111213212223313233
T0.1076 Å20.0069 Å2-0.0037 Å2-0.0965 Å20.0019 Å2--0.093 Å2
L1.8597 °2-1.5503 °2-1.1417 °2-1.7814 °21.0375 °2--1.9875 °2
S-0.0093 Å °-0.0812 Å °0.0861 Å °0.0373 Å °0.012 Å °-0.1121 Å °-0.0301 Å °-0.0097 Å °-0.0009 Å °
Refinement TLS groupSelection details: all

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