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- PDB-310d: Crystal structure of 2'-O-Me(CGCGCG)2: an RNA duplex at 1.3 A res... -

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Basic information

Entry
Database: PDB / ID: 310d
TitleCrystal structure of 2'-O-Me(CGCGCG)2: an RNA duplex at 1.3 A resolution. Hydration pattern of 2'-O-methylated RNA
ComponentsRNA (5'-R(*(OMC)P*(OMG)P*(OMC)P*(OMG)P*(OMC)P*(OMG))-3')
KeywordsRNA / A-RNA / DOUBLE HELIX / MODIFIED
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsAdamiak, D.A. / Milecki, J. / Adamiak, R.W. / Dauter, Z. / Rypniewski, W.R.
Citation
Journal: Nucleic Acids Res. / Year: 1997
Title: Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA.
Authors: Adamiak, D.A. / Milecki, J. / Popenda, M. / Adamiak, R.W. / Dauter, Z. / Rypniewski, W.R.
#1: Journal: To be Published
Title: Low Salt NMR Study of R(CGCGCG) and 2'-O-Me(CGCGCG) Reveals Structure of RNA Duplexes Containing Consecutive CG Base Pairs
Authors: Popenda, M. / Biala, E. / Milecki, J. / Adamiak, R.W.
History
DepositionMay 25, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 24, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / struct_conn / struct_ref / struct_ref_seq
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 21, 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*(OMC)P*(OMG)P*(OMC)P*(OMG)P*(OMC)P*(OMG))-3')
B: RNA (5'-R(*(OMC)P*(OMG)P*(OMC)P*(OMG)P*(OMC)P*(OMG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0294
Polymers3,9812
Non-polymers492
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.270, 26.270, 160.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-13-

MG

21A-22-

HOH

31A-33-

HOH

41B-23-

HOH

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Components

#1: RNA chain RNA (5'-R(*(OMC)P*(OMG)P*(OMC)P*(OMG)P*(OMC)P*(OMG))-3')


Mass: 1990.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#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


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal
*PLUS
Density % sol: 47 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlRNA1drop
250 mMHEPES1drop
315 mM1dropprecipitantMgCl2
41 mMspermine tetrahydrochloride1dropprecipitant
530-40 %MPD1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 1995 / Details: SEGMENTED MIRROR
RadiationMonochromator: TRIANGULAR GE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.3→8 Å / Num. obs: 8165 / % possible obs: 95.3 % / Redundancy: 11 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 32
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3.2 / % possible all: 91.9
Reflection
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 8 Å / % possible obs: 95.3 % / Num. measured all: 96765
Reflection shell
*PLUS
% possible obs: 91.9 % / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
AMoREphasing
SHELXL-96refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ARN035

Resolution: 1.3→8 Å / Num. parameters: 2778 / Num. restraintsaints: 3275 / σ(F): 0 / Stereochemistry target values: CCP4 DICTIONARY
RfactorNum. reflection% reflection
obs0.172 8165 95.3 %
all-8165 -
Solvent computationSolvent model: MOEWS, KRETSINGER, J.MOL.BIOL. 91(1973)201
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 295 / Occupancy sum non hydrogen: 154
Refinement stepCycle: LAST / Resolution: 1.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 370 50 44 464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.025
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.098
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.032
X-RAY DIFFRACTIONs_approx_iso_adps0.085
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 8 Å / Num. reflection obs: 6979 / Rfactor all: 0.175 / Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS

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