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- PDB-4glc: DNA dodecamer containing 5-hydroxymethyl-cytosine -

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Basic information

Entry
Database: PDB / ID: 4glc
TitleDNA dodecamer containing 5-hydroxymethyl-cytosine
ComponentsDNA (5'-D(*CP*GP*(5HC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA dodecamer / epigenetics / 5-hydroxymethyl cytosine
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.831 Å
AuthorsSpingler, B. / Renciuk, D. / Vorlickova, M.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.
Authors: Renciuk, D. / Blacque, O. / Vorlickova, M. / Spingler, B.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Dec 4, 2013Group: Database references
Revision 1.3Sep 13, 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: DNA (5'-D(*CP*GP*(5HC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*(5HC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3872
Polymers7,3872
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-5 kcal/mol
Surface area4550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.513, 41.602, 66.044
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 DNA (5'-D(*CP*GP*(5HC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Mass: 3693.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.98 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / pH: 7
Details: 0.04M sodium cacodylate buffer, 0.08M sodium chloride, 0.012M spermine tetra hydrochloride, 30% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00067
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 9, 2012
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00067 Å / Relative weight: 1
ReflectionResolution: 1.831→41.6 Å / Num. obs: 6201 / % possible obs: 97.5 % / Redundancy: 3.68 % / Rmerge(I) obs: 0.034 / Rsym value: 0.021 / Net I/σ(I): 24.06
Reflection shellResolution: 1.831→1.94 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.65 / % possible all: 96.6

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Processing

Software
NameClassification
RemDAqdata collection
PHASERphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DPN

1dpn


Resolution: 1.831→35.2 Å / Num. parameters: 2123 / Num. restraintsaints: 2406 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.306 435 7.015 %RANDOM
Rwork0.233 ---
all0.251 6201 --
obs0.233 6119 97.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 528.6
Refinement stepCycle: LAST / Resolution: 1.831→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 0 40 530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.012
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.006
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.07
X-RAY DIFFRACTIONs_approx_iso_adps0

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