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- PDB-9aus: Crystal structure of loop-closed dumbbell RNA bridged by glycine -

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Basic information

Entry
Database: PDB / ID: 9aus
TitleCrystal structure of loop-closed dumbbell RNA bridged by glycine
Components
  • Fab BL3-6 heavy chain
  • Fab BL3-6 light chain
  • Loop-closed dumbbell RNA bridged by glycine
KeywordsRNA / RNA aminoacylation / T-loop / glycine-bridged flexizyme
Function / homologyGLYCINE / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsRadakovic, A. / Lewicka, A. / Todisco, M. / Aitken, H.R.M. / Weiss, Z. / Kim, S. / Bannan, A. / Piccirilli, J.A. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149336 United States
Simons Foundation290363 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: A potential role for RNA aminoacylation prior to its role in peptide synthesis.
Authors: Radakovic, A. / Lewicka, A. / Todisco, M. / Aitken, H.R.M. / Weiss, Z. / Kim, S. / Bannan, A. / Piccirilli, J.A. / Szostak, J.W.
History
DepositionFeb 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab BL3-6 heavy chain
L: Fab BL3-6 light chain
R: Loop-closed dumbbell RNA bridged by glycine
A: Fab BL3-6 heavy chain
B: Fab BL3-6 light chain
C: Loop-closed dumbbell RNA bridged by glycine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,40313
Polymers108,7526
Non-polymers6517
Water6,990388
1
H: Fab BL3-6 heavy chain
L: Fab BL3-6 light chain
R: Loop-closed dumbbell RNA bridged by glycine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7397
Polymers54,3763
Non-polymers3634
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fab BL3-6 heavy chain
B: Fab BL3-6 light chain
C: Loop-closed dumbbell RNA bridged by glycine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6646
Polymers54,3763
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.514, 82.085, 92.668
Angle α, β, γ (deg.)63.950, 88.690, 88.400
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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RNA chain , 1 types, 2 molecules RC

#3: RNA chain Loop-closed dumbbell RNA bridged by glycine


Mass: 7128.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Antibody , 2 types, 4 molecules HALB

#1: Antibody Fab BL3-6 heavy chain


Mass: 23852.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab BL3-6 light chain


Mass: 23394.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 395 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.2 M Lithium sulfate monohydrate, 20% w/v Polyethylene glycol 3,350,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.07→46.07 Å / Num. obs: 57272 / % possible obs: 91.14 % / Redundancy: 3.9 % / Biso Wilson estimate: 39.77 Å2 / CC1/2: 0.992 / Net I/σ(I): 6.55
Reflection shellResolution: 2.07→2.144 Å / Num. unique obs: 5776 / CC1/2: 0.591

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Processing

Software
NameVersionClassification
PHASER1.20.1_4487phasing
PHENIX1.20.1_4487refinement
PHASER1.20.1_4487phasing
MOSFLM1.20.1_4487data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→46.07 Å / SU ML: 0.3183 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.8501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2538 2034 3.58 %
Rwork0.2211 54849 -
obs0.2222 56883 91.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.11 Å2
Refinement stepCycle: LAST / Resolution: 2.07→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 953 34 388 8017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00267890
X-RAY DIFFRACTIONf_angle_d0.576110935
X-RAY DIFFRACTIONf_chiral_restr0.04111255
X-RAY DIFFRACTIONf_plane_restr0.00391224
X-RAY DIFFRACTIONf_dihedral_angle_d12.51162952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.110.33451290.30253735X-RAY DIFFRACTION91.91
2.11-2.170.34671360.29553676X-RAY DIFFRACTION92.32
2.17-2.230.3681380.2953744X-RAY DIFFRACTION93.72
2.23-2.290.34081390.29483733X-RAY DIFFRACTION92.17
2.29-2.370.30811380.28993719X-RAY DIFFRACTION93.14
2.37-2.450.32241390.28843694X-RAY DIFFRACTION92.27
2.45-2.550.3211370.27073695X-RAY DIFFRACTION91.94
2.55-2.660.31141250.27553646X-RAY DIFFRACTION91.09
2.66-2.80.30911380.27223555X-RAY DIFFRACTION88.16
2.81-2.980.26491220.2593275X-RAY DIFFRACTION81.35
2.98-3.210.32151480.2483752X-RAY DIFFRACTION93.91
3.21-3.530.28251430.22013793X-RAY DIFFRACTION94.84
3.53-4.040.22121400.19663686X-RAY DIFFRACTION92.26
4.05-5.090.16931270.15923574X-RAY DIFFRACTION89.18
5.1-46.070.19091350.17283572X-RAY DIFFRACTION88.77

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