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- PDB-4qkk: Crystal structure of an oligonucleotide containing 5-formylcytosine -

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Basic information

Entry
Database: PDB / ID: 4qkk
TitleCrystal structure of an oligonucleotide containing 5-formylcytosine
ComponentsDNA (5'-D(*CP*TP*AP*(5FC)P*GP*(5FC)P*GP*(5FC)P*GP*TP*AP*G)-3')
KeywordsDNA / Oligonucleotide / Epigenetic Ten-Eleven / Translocation proteins / Thymine DNA glycosylase / Formylcytosine
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / P-SAD / Resolution: 1.4 Å
AuthorsRaiber, E.-A. / Murat, P. / Chirgadze, D.Y. / Luisi, B.F. / Balasubramanian, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: 5-Formylcytosine alters the structure of the DNA double helix.
Authors: Raiber, E.A. / Murat, P. / Chirgadze, D.Y. / Beraldi, D. / Luisi, B.F. / Balasubramanian, S.
History
DepositionJun 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / pdbx_entity_src_syn / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Mar 20, 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*TP*AP*(5FC)P*GP*(5FC)P*GP*(5FC)P*GP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,7471
Polymers3,7471
Non-polymers00
Water97354
1
A: DNA (5'-D(*CP*TP*AP*(5FC)P*GP*(5FC)P*GP*(5FC)P*GP*TP*AP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)7,4952
Polymers7,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)44.393, 44.393, 46.254
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(*CP*TP*AP*(5FC)P*GP*(5FC)P*GP*(5FC)P*GP*TP*AP*G)-3')


Mass: 3747.422 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.: 54 / 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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.01M magnesium sulphate, 0.05M sodium cacodylate, 1.8M lithium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.4→46.25 Å / Num. all: 9608 / Num. obs: 9608 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 19.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.1715 / Mean I/σ(I) obs: 2 / Num. unique all: 1347 / Rsym value: 0.1715 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHENIX(phenix.refine: 1.9_1692)model building
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: P-SAD / Resolution: 1.4→25.974 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1593 479 5.01 %Random
Rwork0.1401 ---
all0.1411 9567 --
obs0.1411 9567 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→25.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 249 0 54 303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014278
X-RAY DIFFRACTIONf_angle_d1.377427
X-RAY DIFFRACTIONf_dihedral_angle_d23.801101
X-RAY DIFFRACTIONf_chiral_restr0.0844
X-RAY DIFFRACTIONf_plane_restr0.01112
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4-1.60260.2961520.21042954
1.6026-2.0190.1651620.16312986
2.019-25.97840.14651650.12883148

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