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- PDB-471d: CRYSTAL STRUCTURE AND IMPROVED ANTISENSE PROPERTIES OF 2'-O-(2-ME... -

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Basic information

Entry
Database: PDB / ID: 471d
TitleCRYSTAL STRUCTURE AND IMPROVED ANTISENSE PROPERTIES OF 2'-O-(2-METHOXYETHYL)-RNA
ComponentsRNA (5'-R(*(C43)P*(G48)P*(C43)P*(G48)P*(A44)P*(A44)P*(U36)P*(U36)P*(C43)P*(G48)P*(C43)P*(G48))-3')
KeywordsRNA / 2'-O-(2-METHOXYETHYL) RIBOSE / RNA DODECAMER DUPLEX / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsTeplova, M. / Minasov, G. / Tereshko, V. / Inamati, G. / Cook, P.D. / Egli, M.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure and improved antisense properties of 2'-O-(2-methoxyethyl)-RNA.
Authors: Teplova, M. / Minasov, G. / Tereshko, V. / Inamati, G.B. / Cook, P.D. / Manoharan, M. / Egli, M.
History
DepositionApr 29, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0May 12, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2013Group: Atomic model
Revision 1.4Feb 27, 2013Group: Atomic model
Revision 2.0Feb 28, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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: RNA (5'-R(*(C43)P*(G48)P*(C43)P*(G48)P*(A44)P*(A44)P*(U36)P*(U36)P*(C43)P*(G48)P*(C43)P*(G48))-3')
B: RNA (5'-R(*(C43)P*(G48)P*(C43)P*(G48)P*(A44)P*(A44)P*(U36)P*(U36)P*(C43)P*(G48)P*(C43)P*(G48))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0974
Polymers9,0492
Non-polymers492
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.06, 35.400, 48.340
Angle α, β, γ (deg.)90.00, 95.00, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-101-

MG

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Components

#1: RNA chain RNA (5'-R(*(C43)P*(G48)P*(C43)P*(G48)P*(A44)P*(A44)P*(U36)P*(U36)P*(C43)P*(G48)P*(C43)P*(G48))-3')


Mass: 4524.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: O2* OF EACH RIBOSE MODIFIED BY METHOXYETHYL
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growpH: 7.5
Details: DROPLETS CONTAINING 2MM OLIGONUCLEOTIDE, 50 MM MGCL2, 50 MM NA HEPES PH 7.5, 15% PEG 400, AGAINST 1 ML OF RESERVOIR SOLUTION CONTAINING 100 MM MGCL2, 100 MM NA HEPES PH 7.5, 30% PEG 400
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2NA HEPES11
3PEG 40011
4MGCL212
5NA HEPES12
6PEG 40012
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mMRNA1drop
250 mMNa-HEPES1reservoirpH7.5
350-100 mM1reservoirMgCl2
415 %(v/v)PEG4001reservoir
51
61

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 3, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 2129 / Num. obs: 2129 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.072
Reflection
*PLUS
Num. measured all: 11424

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.252 -10 %RANDOM
Rwork0.193 ---
obs0.193 1881 92.8 %-
all-2129 --
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 602 2 12 616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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