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

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Basic information

Entry
Database: PDB / ID: 4hli
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 / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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
DepositionOct 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4504
Polymers7,3872
Non-polymers632
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-7 kcal/mol
Surface area4470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.175, 40.590, 65.399
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.) Homo sapiens (human)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.04m sodium cacodylate buffer, 0.08M NaCCl, 0.12m KCl, 0.02m MgCl2, 0.012m spermine tetra hydrochloride, 35% 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 / Wavelength: 1.00067 Å
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 wavelength
IDWavelength (Å)Relative weight
11.000671
21.000671
ReflectionResolution: 1.99→50 Å / Num. all: 4775 / Num. obs: 4315 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.55 % / Rmerge(I) obs: 0.038 / Rsym value: 0.022 / Net I/σ(I): 21.23
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 5.81 / % possible all: 94.6

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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: 1.99→50 Å / Num. parameters: 2099 / Num. restraintsaints: 2456 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3281 334 6.99 %RANDOM
Rwork0.2518 ---
all0.2548 4775 --
obs0.2518 4315 96.5 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 515.5
Refinement stepCycle: LAST / Resolution: 1.99→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 2 29 521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.073
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0005
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.006
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.075
X-RAY DIFFRACTIONs_approx_iso_adps0

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