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- PDB-4glg: DNA dodecamer containing 5-methyl cytosine -

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Basic information

Entry
Database: PDB / ID: 4glg
TitleDNA dodecamer containing 5-methyl cytosine
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3')
KeywordsDNA / B-DNA dodecamer / epigenetics / 5-methyl cytosine
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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*CP*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3552
Polymers7,3552
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint4 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.744, 41.885, 66.062
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*CP*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3')


Mass: 3677.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 298 K / pH: 7
Details: 0.04M sodium cacodylate buffer, 0.08M sodium chloride, 0.012M spermine tetra hydrochloride, 27% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00067
DetectorType: DECTRIS PILATUS 2M-F / 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: 1.72→41.92 Å / Num. obs: 7618 / % possible obs: 97.9 % / Redundancy: 3.65 % / Rmerge(I) obs: 0.024 / Rsym value: 0.015 / Net I/σ(I): 28.99
Reflection shellResolution: 1.72→1.82 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 6.94 / % possible all: 96.1

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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: 1.72→41.9 Å / Num. parameters: 4774 / Num. restraintsaints: 10807 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.287 458 6.012 %RANDOM
Rwork0.22 ---
all0.222 7618 --
obs0.22 -97.9 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 558.6
Refinement stepCycle: LAST / Resolution: 1.72→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 488 0 88 576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0085
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0164
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.007
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0077
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0074
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0274
X-RAY DIFFRACTIONs_approx_iso_adps0

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