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- PDB-1ma8: A-DNA decamer GCGTA(UMS)ACGC with incorporated 2'-methylseleno-uridine -

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Basic information

Entry
Database: PDB / ID: 1ma8
TitleA-DNA decamer GCGTA(UMS)ACGC with incorporated 2'-methylseleno-uridine
Components5'-D(*GP*CP*GP*TP*AP*UMSP*AP*CP*GP*C)-3'
KeywordsDNA / 2'-methylseleno-uridine
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsTeplova, M. / Wilds, C.J. / Wawrzak, Z. / Tereshko, V. / Du, Q. / Carrasco, N. / Huang, Z. / Egli, M.
CitationJournal: BIOCHIMIE / Year: 2002
Title: Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: proof of principle
Authors: Teplova, M. / Wilds, C.J. / Wawrzak, Z. / Tereshko, V. / Du, Q. / Carrasco, N. / Huang, Z. / Egli, M.
History
DepositionAug 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*UMSP*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*AP*UMSP*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,2482
Polymers6,2482
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.555, 43.967, 45.340
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*UMSP*AP*CP*GP*C)-3'


Mass: 3123.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: U-Se-modified DNA duplex
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.88 Å3/Da / Density % sol: 34.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, spermine tetrahydrochloride, potassium chloride, sodium chloride, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2spermine tetrahydrochloride11
3KCl11
4NaClSodium chloride11
5sodium cacodylate11
6MPD12
7NaClSodium chloride12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mMDNA solution1drop
240 mMsodium cacodylate1droppH7.0
312 mM1dropNaCl
480 mM1dropKCl
512 mMspermine tetrahydrochloride1drop
610 %(v/v)1drop
735 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B
DetectorType: MARRESEARCH / Detector: CCD / Date: May 30, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 23332 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rsym value: 0.049
Reflection shellResolution: 1.3→1.35 Å / Rsym value: 0.263 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.263

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→10 Å / σ(I): 4
RfactorNum. reflectionSelection details
Rfree0.173 1048 random
Rwork0.149 --
obs-21189 -
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 628 0 141 769
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_bond_d0.015
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection all: 23279 / % reflection Rfree: 5 % / Rfactor obs: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS

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