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- PDB-3ok2: Crystal structure of the ANA:RNA decamer without lattice transloc... -

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Basic information

Entry
Database: PDB / ID: 3ok2
TitleCrystal structure of the ANA:RNA decamer without lattice translocation defects
Components
  • (A6C)(A6C)(A6G)(A6U)(A6A)(A6A)(A6U)(A6G)(A6C)(A6C)(PO4)
  • GGCAUUACGG
KeywordsRNA / hybrid / ANA / sugar modification / altritol sugar rings
Function / homologyOTHER / OTHER (> 10) / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.963 Å
AuthorsOvaere, M. / Van Meervelt, L.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex.
Authors: Ovaere, M. / Sponer, J. / Sponer, J.E. / Herdewijn, P. / Van Meervelt, L.
History
DepositionAug 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Dec 12, 2018Group: Advisory / Data collection / Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Revision 1.3Feb 21, 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.pdbx_value_order / _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: (A6C)(A6C)(A6G)(A6U)(A6A)(A6A)(A6U)(A6G)(A6C)(A6C)(PO4)
C: (A6C)(A6C)(A6G)(A6U)(A6A)(A6A)(A6U)(A6G)(A6C)(A6C)(PO4)
E: (A6C)(A6C)(A6G)(A6U)(A6A)(A6A)(A6U)(A6G)(A6C)(A6C)(PO4)
B: GGCAUUACGG
D: GGCAUUACGG
F: GGCAUUACGG


Theoretical massNumber of molelcules
Total (without water)19,7136
Polymers19,7136
Non-polymers00
Water4,306239
1
A: (A6C)(A6C)(A6G)(A6U)(A6A)(A6A)(A6U)(A6G)(A6C)(A6C)(PO4)
B: GGCAUUACGG


Theoretical massNumber of molelcules
Total (without water)6,5712
Polymers6,5712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: (A6C)(A6C)(A6G)(A6U)(A6A)(A6A)(A6U)(A6G)(A6C)(A6C)(PO4)
D: GGCAUUACGG


Theoretical massNumber of molelcules
Total (without water)6,5712
Polymers6,5712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: (A6C)(A6C)(A6G)(A6U)(A6A)(A6A)(A6U)(A6G)(A6C)(A6C)(PO4)
F: GGCAUUACGG


Theoretical massNumber of molelcules
Total (without water)6,5712
Polymers6,5712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.070, 42.510, 157.790
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: Other (A6C)(A6C)(A6G)(A6U)(A6A)(A6A)(A6U)(A6G)(A6C)(A6C)(PO4)


Mass: 3354.144 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Molecule was synthesized
#2: RNA chain GGCAUUACGG


Mass: 3216.973 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Molecule was synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.01M NiCl2, 1.0M Li2SO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→39.45 Å / Num. all: 11922 / Num. obs: 11922 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.066 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Num. unique allRsym valueDiffraction-ID% possible all
1.96-2.0717750.607193.7
2.07-2.1916340.403191.7
2.78-3.111870.068189.8
3.1-3.5810490.055187.9
4.39-6.217030.062186.4
6.21-39.4473730.045174.045

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.963→39.45 Å / Cor.coef. Fo:Fc: 0.964 / SU B: 4.726 / SU ML: 0.129 / σ(F): 0 / ESU R: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rwork0.22443 ---
all0.22443 11880 --
obs0.22443 11880 89.23 %-
Rfree---NONE
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.538 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---0.95 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.963→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1302 0 239 1541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.50832229
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02618
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8441.51
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it3.60431446
X-RAY DIFFRACTIONr_scangle_it4.5384.52229
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.963→2.014 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.348 902 -
obs--90.56 %

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