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- PDB-1mlx: Crystal Structure Analysis of a 2'-O-[2-(Methylthio)-ethyl]-Modif... -

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Basic information

Entry
Database: PDB / ID: 1mlx
TitleCrystal Structure Analysis of a 2'-O-[2-(Methylthio)-ethyl]-Modified Oligodeoxynucleotide Duplex
Components5'-D(*GP*CP*GP*TP*AP*SMTP*AP*CP*GP*C)-3'
KeywordsDNA / DOUBLE HELIX / A-FORM / ANTISENSE MODIFICATION / NUCLEIC ACID ANALOGUE / RNA AFFINITY / NUCLEASE RESISTANCE / PROTEIN BINDING AFFINITY / HIGH RESOLUTION STRUCTURE / HYDRATION
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPrakash, T.P. / Manoharan, M. / Kawasaki, A.M. / Fraser, A.S. / Lesnik, E.A. / Sioufi, N. / Leeds, J.M. / Teplova, M. / Egli, M.
CitationJournal: Biochemistry / Year: 2002
Title: 2'-O-[2-(Methylthio)ethyl]-Modified Oligonucleotide: An Analogue of 2'-O-[2-(Methoxy)-ethyl]-Modified Oligonucleotide with Improved Protein Binding Properties and High Binding Affinity to Target RNA
Authors: Prakash, T.P. / Manoharan, M. / Kawasaki, A.M. / Fraser, A.S. / Lesnik, E.A. / Sioufi, N. / Leeds, J.M. / Teplova, M. / Egli, M.
History
DepositionAug 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_comp_id / _struct_conn.ptnr2_label_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*SMTP*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*AP*SMTP*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,2702
Polymers6,2702
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.728, 44.473, 46.229
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*SMTP*AP*CP*GP*C)-3'


Mass: 3135.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid phase oligonucleotide synthesis
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.95 Å3/Da / Density % sol: 36.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium cacodylate, potassium chloride, spermine tetrahydrochloride, 2-methyl-2,4-pentanediol (MPD), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2KCl11
3spermine tetrahydrochloride11
4MPD11
5KCl12
6MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mMoligonucleotide1dropin water
240 mMsodium cacodylate1droppH7.0
380 mM1dropKCl
412 mMspermine tetrahydrochloride1drop
510 %(v/v)MPD1drop
635 %(v/v)1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→20 Å / Num. all: 14088 / Num. obs: 12796 / % possible obs: 95.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.03
Reflection shellResolution: 1.25→1.29 Å / Rmerge(I) obs: 0.313 / Num. unique all: 1341 / % possible all: 93.6
Reflection
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 15 Å / Num. obs: 14054 / % possible obs: 96.7 % / Rmerge(I) obs: 0.141

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Processing

Software
NameClassification
XDSdata scaling
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→15 Å / σ(F): 4 / σ(I): 2 /
RfactorNum. reflection
all0.141 14054
obs0.137 12784
Refinement stepCycle: LAST / Resolution: 1.25→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 635 0 146 781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.029
X-RAY DIFFRACTIONs_angle_d0.034
LS refinement shellHighest resolution: 1.25 Å / Rfactor Rwork: 0.141
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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