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- PDB-4qc7: Dodecamer structure of 5-formylcytosine containing DNA -

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Basic information

Entry
Database: PDB / ID: 4qc7
TitleDodecamer structure of 5-formylcytosine containing DNA
Componentsshort DNA strands
KeywordsDNA / double helix / B-form DNA / 5-formylcytosine
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSzulik, M.W. / Pallan, P. / Egli, M. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2015
Title: Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.
Authors: Szulik, M.W. / Pallan, P.S. / Nocek, B. / Voehler, M. / Banerjee, S. / Brooks, S. / Joachimiak, A. / Egli, M. / Eichman, B.F. / Stone, M.P.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: short DNA strands
B: short DNA strands


Theoretical massNumber of molelcules
Total (without water)7,3832
Polymers7,3832
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint3 kcal/mol
Surface area4260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.095, 41.476, 65.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain short DNA strands


Mass: 3691.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized nucleic acid.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5% MPD, 20 mM Na Cacodylate, 6 mM Spermine tetra-HCl, 6 mM NaCl, 40 mM KCl , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 5842 / Num. obs: 5801 / % possible obs: 99.3 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 60
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 3.25 / % possible all: 100

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBL (with LS-CAT developed extensions)data collection
MOLREPphasing
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 436D

436d


Resolution: 1.9→35.07 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.094 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(I): 5 / ESU R: 0.172 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24529 413 7.2 %RANDOM
Rwork0.22637 ---
obs0.22767 5362 99.35 %-
all-5842 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.9→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 0 17 507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.011548
X-RAY DIFFRACTIONr_bond_other_d0.0020.02268
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.295842
X-RAY DIFFRACTIONr_angle_other_deg1.4673634
X-RAY DIFFRACTIONr_chiral_restr0.080.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.02292
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02118
X-RAY DIFFRACTIONr_scbond_it5.9874.947548
X-RAY DIFFRACTIONr_scbond_other5.9914.948547
X-RAY DIFFRACTIONr_scangle_other7.8967.424843
X-RAY DIFFRACTIONr_long_range_B_refined7.72546.792786
X-RAY DIFFRACTIONr_long_range_B_other7.72146.813780
LS refinement shellResolution: 1.897→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 33 -
Rwork0.314 380 -
obs-380 99.04 %

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