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- PDB-3ey2: A Conformational Transition in the Structure of a 2'-Thiomethyl-M... -

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Basic information

Entry
Database: PDB / ID: 3ey2
TitleA Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution
Components5'-D(*GP*CP*GP*TP*AP*(USM)P*AP*CP*GP*C)-3'
KeywordsDNA / 2'-Thiomethyl modified DNA / modified sugar / nucleic acid structure.
Function / homologyN-methylpropane-1,3-diamine / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsEgli, M. / Pallan, P.S.
CitationJournal: Chem.Commun.(Camb.) / Year: 2009
Title: A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.
Authors: Pallan, P.S. / Prakash, T.P. / Li, F. / Eoff, R.L. / Manoharan, M. / Egli, M.
History
DepositionOct 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: 5'-D(*GP*CP*GP*TP*AP*(USM)P*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*AP*(USM)P*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2423
Polymers6,1542
Non-polymers881
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-3 kcal/mol
Surface area3940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.690, 42.920, 46.120
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 5'-D(*GP*CP*GP*TP*AP*(USM)P*AP*CP*GP*C)-3'


Mass: 3077.070 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Chemically synthesized modified DNA (oligonucleotide)
#2: Chemical ChemComp-N3D / N-methylpropane-1,3-diamine


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% MPD, 20 mM Sodium Cacodylate (pH 7.0), 6 mM Spermine tetra-HCl, 40 mM Potassium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Sodium Cacodylate11
3Spermine tetra-HCl11
4Potassium Chloride11
5MPD12
6Sodium Cacodylate12
7Spermine tetra-HCl12
8Potassium Chloride12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9788 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.04→30 Å / Num. all: 24305 / Num. obs: 23179 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057 / Net I/σ(I): 44.12
Reflection shellResolution: 1.04→1.09 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 13.03 / Num. unique all: 2774

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Processing

Software
NameClassification
MAR345data collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 411D

411d


Resolution: 1.04→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1526 1158 -Random
Rwork0.1251 ---
obs0.1251 22026 100 %-
all-23179 --
Refinement stepCycle: LAST / Resolution: 1.04→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 428 6 133 567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.031

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