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- PDB-469d: CRYSTAL STRUCTURE AND IMPROVED ANTISENSE PROPERTIES OF 2'-O-(2-ME... -

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Basic information

Entry
Database: PDB / ID: 469d
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
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jan 16, 2013Group: Atomic model
Revision 1.5Feb 27, 2013Group: Atomic model
Revision 1.6Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.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: 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)9,0733
Polymers9,0492
Non-polymers241
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.20, 34.440, 46.620
Angle α, β, γ (deg.)90.00, 92.40, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-100-

MG

21A-190-

HOH

31B-104-

HOH

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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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.83 Å3/Da / Density % sol: 32.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: DROPLETS CONTAINING 2MM OLIGONUCLEOTIDE, 50 MM MGCL2, 50 MM NA HEPES PH 6.2, 15% PEG 400, AGAINST 1 ML OF RESERVOIR SOLUTION CONTAINING 100 MM MGCL2, 100 MM NA HEPES PH 6.2, 30% PEG 400, ...Details: DROPLETS CONTAINING 2MM OLIGONUCLEOTIDE, 50 MM MGCL2, 50 MM NA HEPES PH 6.2, 15% PEG 400, AGAINST 1 ML OF RESERVOIR SOLUTION CONTAINING 100 MM MGCL2, 100 MM NA HEPES PH 6.2, 30% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2NA HEPES11
3PEG 40011
4MGCL212
5NA HEPES12
6PEG 40012
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mMRNA1drop
250 mMNa-HEPES1reservoirpH6.2
350 mM1reservoirMgCl2
415 %(v/v)PEG4001reservoir
51
61

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 7, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 7032 / Num. obs: 7032 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.055
Reflection
*PLUS
Num. measured all: 39271

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.258 -10 %RANDOM
Rwork0.206 ---
obs0.206 6412 88.7 %-
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 602 1 105 708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.89
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

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