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- PDB-6jv5: Crystal structure of 5-methylcytosine containing decamer dsDNA -

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Basic information

Entry
Database: PDB / ID: 6jv5
TitleCrystal structure of 5-methylcytosine containing decamer dsDNA
ComponentsDNA (5'-D(*CP*CP*AP*GP*(5CM)P*GP*CP*TP*GP*G)-3')
KeywordsDNA / Methylation / cytosine / duplex
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.401 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 18, 2019Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
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

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*AP*GP*(5CM)P*GP*CP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,0601
Polymers3,0601
Non-polymers00
Water1,38777
1
A: DNA (5'-D(*CP*CP*AP*GP*(5CM)P*GP*CP*TP*GP*G)-3')

A: DNA (5'-D(*CP*CP*AP*GP*(5CM)P*GP*CP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,1202
Polymers6,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2220 Å2
ΔGint1 kcal/mol
Surface area3590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.606, 25.788, 34.215
Angle α, β, γ (deg.)90.00, 115.93, 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*(5CM)P*GP*CP*TP*GP*G)-3')


Mass: 3060.019 Da / Num. of mol.: 1
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.02M Magnesium chloride hexahydrate,0.04MSodium cacodylate trihydrate pH 5.5, 40% MPD,0.002M Hexammine cobalt(III) chloride

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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: MAR CCD 130 mm / Detector: CCD / Date: Jan 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 4932 / % possible obs: 99.1 % / Redundancy: 6.6 % / Net I/σ(I): 29.5
Reflection shellResolution: 1.4→1.45 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.401→30.769 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 15.62
RfactorNum. reflection% reflection
Rfree0.2166 240 4.87 %
Rwork0.1805 --
obs0.1824 4932 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.401→30.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 203 0 77 280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005227
X-RAY DIFFRACTIONf_angle_d0.933345
X-RAY DIFFRACTIONf_dihedral_angle_d34.996107
X-RAY DIFFRACTIONf_chiral_restr0.04739
X-RAY DIFFRACTIONf_plane_restr0.00810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4011-1.76530.24231160.16272334X-RAY DIFFRACTION99
1.7653-30.77690.21011240.18572358X-RAY DIFFRACTION99

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