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- PDB-5vcf: RNA hairpin structure containing tetraloop/receptor motif, comple... -

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Basic information

Entry
Database: PDB / ID: 5vcf
TitleRNA hairpin structure containing tetraloop/receptor motif, complexed with 2-MeImpG analogue
Components
  • RNA (5'-R(*CP*UP*AP*UP*GP*CP*CP*UP*GP*CP*UP*G)-3')
  • RNA (5'-R(*CP*UP*GP*CP*UP*GP*GP*CP*UP*AP*AP*GP*GP*CP*CP*CP*GP*AP*AP*AP*GP*G)-3')
KeywordsRNA / tetraloop/receptor
Function / homologyChem-8OS / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, W. / Szostak, J.W.
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
DepositionMar 31, 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 1.2Oct 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 (5'-R(*CP*UP*GP*CP*UP*GP*GP*CP*UP*AP*AP*GP*GP*CP*CP*CP*GP*AP*AP*AP*GP*G)-3')
B: RNA (5'-R(*CP*UP*AP*UP*GP*CP*CP*UP*GP*CP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3053
Polymers10,8782
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-6 kcal/mol
Surface area6120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.073, 71.073, 71.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: RNA chain RNA (5'-R(*CP*UP*GP*CP*UP*GP*GP*CP*UP*AP*AP*GP*GP*CP*CP*CP*GP*AP*AP*AP*GP*G)-3')


Mass: 7112.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*CP*UP*AP*UP*GP*CP*CP*UP*GP*CP*UP*G)-3')


Mass: 3765.256 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

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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: 3.2 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM MgCl2, 200 mM Lithium sulfate monohydrate, 100 mM BIS-TRIS pH 7.0, 25% w/v Polyethylene glycol 3,350

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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: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 3296 / % possible obs: 99.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Rsym value: 0.058 / Χ2: 1.08 / Net I/av σ(I): 17.4 / Net I/σ(I): 0.98
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 316 / CC1/2: 0.886 / Rsym value: 0.495 / Χ2: 0.512 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNJ

4fnj


Resolution: 2.8→46.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.955 / SU B: 12.233 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.997 / ESU R Free: 0.295 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21335 142 4.3 %RANDOM
Rwork0.16313 ---
obs0.16517 3154 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å2-0 Å2
2--0.19 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 2.8→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 719 29 0 748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.012834
X-RAY DIFFRACTIONr_bond_other_d0.0050.02350
X-RAY DIFFRACTIONr_angle_refined_deg1.891.3421296
X-RAY DIFFRACTIONr_angle_other_deg1.7393.023845
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_restr0.1080.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02422
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_it6.3866.838834
X-RAY DIFFRACTIONr_scbond_other6.3876.845835
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.71610.2551297
X-RAY DIFFRACTIONr_long_range_B_refined10.81268.9471168
X-RAY DIFFRACTIONr_long_range_B_other10.84769.0051169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.799→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 11 -
Rwork0.31 221 -
obs--100 %

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