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- PDB-7q81: Crystal structure of the methyltransferase-ribozyme 1, 2'-Selenom... -

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Basic information

Entry
Database: PDB / ID: 7q81
TitleCrystal structure of the methyltransferase-ribozyme 1, 2'-Selenomethyl-Uridine modified (with 1-methyl-adenosine)
Components
  • RNA 2
  • RNA 3
  • RNA1
KeywordsRNA / MTR1 / methyltransferase ribozyme / ribozyme
Function / homologyGUANINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMieczkowski, M. / Hoebartner, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Structure and mechanism of the methyltransferase ribozyme MTR1.
Authors: Scheitl, C.P.M. / Mieczkowski, M. / Schindelin, H. / Hobartner, C.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 11, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA1
B: RNA 2
C: RNA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1859
Polymers19,9123
Non-polymers2736
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-29 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.085, 71.085, 83.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain RNA1


Mass: 4514.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA 2


Mass: 7641.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA 3


Mass: 7755.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 24 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 36-42% MPD, 50mM MES pH 6.4-6.7, 100mM NaCl, 100mM LiCl, 10mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.85→43.07 Å / Num. obs: 5365 / % possible obs: 99.9 % / Redundancy: 24.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0685 / Net I/σ(I): 27.07
Reflection shellResolution: 2.85→2.95 Å / Mean I/σ(I) obs: 1.38 / Num. unique obs: 515 / CC1/2: 0.693 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q7X

7q7x


Resolution: 2.85→43.07 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 456 4.78 %
Rwork0.1877 --
obs0.189 5365 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1313 34 0 1347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011496
X-RAY DIFFRACTIONf_angle_d0.2872341
X-RAY DIFFRACTIONf_dihedral_angle_d9.792716
X-RAY DIFFRACTIONf_chiral_restr0.016305
X-RAY DIFFRACTIONf_plane_restr0.00163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.260.30071540.30633021X-RAY DIFFRACTION100
3.26-4.110.27521490.24413026X-RAY DIFFRACTION100
4.11-36.020.18611530.15713038X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 45.3464 Å / Origin y: 12.9391 Å / Origin z: 42.3798 Å
111213212223313233
T0.7607 Å20.0072 Å20.0461 Å2-0.9115 Å20.0714 Å2--0.6746 Å2
L3.7948 °23.5926 °2-2.2389 °2-6.0191 °2-2.235 °2--2.8256 °2
S0.4952 Å °-0.3426 Å °0.0005 Å °0.1117 Å °-0.6062 Å °-0.175 Å °-0.0333 Å °0.6551 Å °0.0674 Å °
Refinement TLS groupSelection details: all

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