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- PDB-6jv3: Crystal structure of 5-hydoxylmethylcytosine containing decamer dsDNA -

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Basic information

Entry
Database: PDB / ID: 6jv3
TitleCrystal structure of 5-hydoxylmethylcytosine containing decamer dsDNA
ComponentsDNA (5'-D(*CP*CP*AP*GP*(5HC)P*GP*CP*TP*GP*G)-3')
KeywordsDNA / 5-hydoxylmethylcytosine / duplex DNA
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.851 Å
AuthorsZhang, L. / Wang, Y.X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21572133 China
National Natural Science Foundation of China21722802 China
CitationJournal: Chem Sci / Year: 2019
Title: Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine.
Authors: Fu, T. / Liu, L. / Yang, Q.L. / Wang, Y. / Xu, P. / Zhang, L. / Liu, S. / Dai, Q. / Ji, Q. / Xu, G.L. / He, C. / Luo, C. / Zhang, L.
History
DepositionApr 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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(*CP*CP*AP*GP*(5HC)P*GP*CP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*(5HC)P*GP*CP*TP*GP*G)-3')
C: DNA (5'-D(*CP*CP*AP*GP*(5HC)P*GP*CP*TP*GP*G)-3')
D: DNA (5'-D(*CP*CP*AP*GP*(5HC)P*GP*CP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,3044
Polymers12,3044
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-9 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.907, 23.818, 85.556
Angle α, β, γ (deg.)90.00, 111.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain
DNA (5'-D(*CP*CP*AP*GP*(5HC)P*GP*CP*TP*GP*G)-3')


Mass: 3076.018 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12

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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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.08M Sodium chloride,0.012M Potassium chloride, 0.02M Magnesium chloride hexahydrate 0.04M Sodium cacodylate trihydrate pH 6.0 30% MPD, 0.012M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 2611 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 16.7
Reflection shellResolution: 2.85→2.95 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.851→26.604 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.15
RfactorNum. reflection% reflection
Rfree0.2821 129 4.94 %
Rwork0.2281 --
obs0.2309 2611 87.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.851→26.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 816 0 0 816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005913
X-RAY DIFFRACTIONf_angle_d1.4231400
X-RAY DIFFRACTIONf_dihedral_angle_d37.386448
X-RAY DIFFRACTIONf_chiral_restr0.176152
X-RAY DIFFRACTIONf_plane_restr0.00540
LS refinement shellResolution: 2.8511→26.6047 Å
RfactorNum. reflection% reflection
Rfree0.2821 129 -
Rwork0.2281 2482 -
obs--87 %

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