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- PDB-5ux3: RNA hairpin structure containing 2-MeImpG monomer analogue and 2-... -

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Basic information

Entry
Database: PDB / ID: 5ux3
TitleRNA hairpin structure containing 2-MeImpG monomer analogue and 2-MeImp-oligomer analogue
Components
  • RNA (25-MER)
  • RNA (5'-D(*(RG))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
KeywordsRNA
Function / homologyChem-8OS / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 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 / 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(*(RG))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2163
Polymers10,7892
Non-polymers4271
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint5 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.527, 46.527, 156.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: RNA chain RNA (25-MER)


Mass: 8238.869 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-D(*(RG))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Mass: 2549.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-8OS / 5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine


Type: RNA linking / Mass: 427.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N7O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.8 Å3/Da / Density % sol: 68.1 %
Crystal growTemperature: 292 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: 2.5→50 Å / Num. obs: 6436 / % possible obs: 98.7 % / Redundancy: 5.1 % / CC1/2: 0.943 / Rmerge(I) obs: 0.08 / Rsym value: 0.067 / Χ2: 1.02 / Net I/σ(I): 20.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1 / Num. unique obs: 604 / CC1/2: 0.754 / Rsym value: 0.463 / Χ2: 0.639 / % possible all: 94.1

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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: 4FNJ

4fnj


Resolution: 2.5→44.61 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.957 / SU B: 13.705 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.232 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26127 281 4.4 %RANDOM
Rwork0.21848 ---
obs0.2204 6154 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.743 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.5→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 714 29 1 744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.013826
X-RAY DIFFRACTIONr_bond_other_d0.0130.022355
X-RAY DIFFRACTIONr_angle_refined_deg2.5641.5521275
X-RAY DIFFRACTIONr_angle_other_deg2.7913.108852
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_restr0.2520.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02433
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02185
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_it78.246826
X-RAY DIFFRACTIONr_scbond_other6.9978.248827
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.46212.3211276
X-RAY DIFFRACTIONr_long_range_B_refined10.27684.2781203
X-RAY DIFFRACTIONr_long_range_B_other10.27584.291204
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.598 18 -
Rwork0.476 423 -
obs--94.43 %

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