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- PDB-5uz6: RNA hairpin structure containing 2-MeImp-oligo analogue -

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Basic information

Entry
Database: PDB / ID: 5uz6
TitleRNA hairpin structure containing 2-MeImp-oligo analogue
Components
  • RNA (25-MER)
  • RNA (5'-D(*(8OS))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
KeywordsRNA / 2-MeIm
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, W. / Oh, S.S. / Szostak, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Aeronautic Space Administration (NASA, United States) United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
Authors: Zhang, W. / Tam, C.P. / Zhou, L. / Oh, S.S. / Wang, J. / Szostak, J.W.
History
DepositionFeb 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (25-MER)
B: RNA (5'-D(*(8OS))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
C: RNA (25-MER)
D: RNA (5'-D(*(8OS))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
E: RNA (25-MER)
F: RNA (5'-D(*(8OS))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,2466
Polymers32,2466
Non-polymers00
Water97354
1
A: RNA (25-MER)
B: RNA (5'-D(*(8OS))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,7492
Polymers10,7492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (25-MER)
D: RNA (5'-D(*(8OS))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,7492
Polymers10,7492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RNA (25-MER)
F: RNA (5'-D(*(8OS))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,7492
Polymers10,7492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.695, 63.066, 65.917
Angle α, β, γ (deg.)90.00, 122.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (25-MER)


Mass: 8199.013 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-D(*(8OS))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Mass: 2549.641 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.91 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM MgCl2, 3 M ammonia sulfate, 100 mM HEPES 7.5

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20855 / % possible obs: 96.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.052 / Rsym value: 0.057 / Χ2: 1.028 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1912 / CC1/2: 0.825 / Rsym value: 0.28 / Χ2: 0.625 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERv3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UX3

5ux3


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.389 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.193 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1027 4.9 %RANDOM
Rwork0.221 ---
obs0.223 19827 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.84 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.02 Å2
2---0.04 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2159 0 54 2213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122406
X-RAY DIFFRACTIONr_bond_other_d0.030.0211020
X-RAY DIFFRACTIONr_angle_refined_deg2.4521.4433729
X-RAY DIFFRACTIONr_angle_other_deg2.4473.0722451
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_restr0.2620.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021248
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02549
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4585.0642403
X-RAY DIFFRACTIONr_scbond_other4.4585.0642404
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.747.5963729
X-RAY DIFFRACTIONr_long_range_B_refined6.29150.2783356
X-RAY DIFFRACTIONr_long_range_B_other6.28350.2753355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 75 -
Rwork0.311 1226 -
obs--81.77 %

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