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- PDB-5zas: Crystal structure of 5-formylcytosine containing decamer dsDNA -

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Basic information

Entry
Database: PDB / ID: 5zas
TitleCrystal structure of 5-formylcytosine containing decamer dsDNA
ComponentsDNA (5'-D(*CP*CP*AP*GP*(5FC)P*GP*CP*TP*GP*G)-3')
KeywordsDNA / Cytosine modification
Function / homologyBICARBONATE ION / DNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsFu, T.R. / Zhang, L.
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
DepositionFeb 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 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 / _citation_author.name
Revision 1.3Mar 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*(5FC)P*GP*CP*TP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*(5FC)P*GP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2704
Polymers6,1482
Non-polymers1222
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint4 kcal/mol
Surface area3480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.548, 54.548, 45.819
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(*CP*CP*AP*GP*(5FC)P*GP*CP*TP*GP*G)-3')


Mass: 3074.002 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 50mM cacodylate pH 6.0, 20mM magnesium acetate, 0.5mM spermine, 100mM NaCl, 25% MPD

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9676 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9676 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 11176 / % possible obs: 99.5 % / Redundancy: 9.8 % / Net I/σ(I): 37.6
Reflection shellResolution: 1.56→1.62 Å

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Processing

Software
NameVersionClassification
PHENIX5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→47.24 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.183 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1621 526 4.7 %RANDOM
Rwork0.14666 ---
obs0.14736 10569 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.583 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.56→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 8 118 534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.012458
X-RAY DIFFRACTIONr_bond_other_d0.0040.02228
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.332690
X-RAY DIFFRACTIONr_angle_other_deg1.5943536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02250
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02110
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0452.165458
X-RAY DIFFRACTIONr_scbond_other2.0592.167459
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5143.257691
X-RAY DIFFRACTIONr_long_range_B_refined2.9722.995805
X-RAY DIFFRACTIONr_long_range_B_other2.22921.616724
X-RAY DIFFRACTIONr_rigid_bond_restr3.1643686
X-RAY DIFFRACTIONr_sphericity_free22.413516
X-RAY DIFFRACTIONr_sphericity_bonded7.9485746
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 51 -
Rwork0.146 760 -
obs--99.51 %

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