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- PDB-5vgw: RNA hairpin structure containing tetraloop/receptor motif -

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Basic information

Entry
Database: PDB / ID: 5vgw
TitleRNA hairpin structure containing tetraloop/receptor motif
Components
  • 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')
  • RNA (5'-R(P*GP*CP*UP*AP*UP*GP*CP*CP*UP*GP*CP*UP*G)-3')
KeywordsRNA / tetraloop/receptor / ligation
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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
DepositionApr 11, 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

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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(P*GP*CP*UP*AP*UP*GP*CP*CP*UP*GP*CP*UP*G)-3')


Theoretical massNumber of molelcules
Total (without water)11,2232
Polymers11,2232
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-8 kcal/mol
Surface area6210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.055, 71.055, 69.781
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(P*GP*CP*UP*AP*UP*GP*CP*CP*UP*GP*CP*UP*G)-3')


Mass: 4110.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM MgCl2, 0.2 M Lithium sulfate monohydrate, 0.1 M 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: Oct 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 4799 / % possible obs: 96.1 % / Redundancy: 3.7 % / CC1/2: 0.914 / Rmerge(I) obs: 0.073 / Rsym value: 0.074 / Χ2: 1.15 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 508 / CC1/2: 0.379 / Rsym value: 0.729 / Χ2: 0.992 / % possible all: 98.8

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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: 2.42→46.15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.961 / SU B: 12.143 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21293 250 5.2 %RANDOM
Rwork0.20727 ---
obs0.20764 4546 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.42→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 746 0 6 752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.011832
X-RAY DIFFRACTIONr_bond_other_d0.0050.02344
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.2781295
X-RAY DIFFRACTIONr_angle_other_deg1.7543834
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_restr0.1010.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02417
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02187
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_it6.6067.253832
X-RAY DIFFRACTIONr_scbond_other6.5737.254831
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.12110.8661296
X-RAY DIFFRACTIONr_long_range_B_refined9.9972.6661103
X-RAY DIFFRACTIONr_long_range_B_other9.98872.6551104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.424→2.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 20 -
Rwork0.366 355 -
obs--98.17 %

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