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- PDB-7q82: Crystal structure of the methyltransferase-ribozyme 1, Thallium d... -

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Basic information

Entry
Database: PDB / ID: 7q82
TitleCrystal structure of the methyltransferase-ribozyme 1, Thallium derivative (with 1-methyl-adenosine)
Components
  • RNA 1
  • RNA 2
  • RNA 3
KeywordsRNA / MTR1 / methyltransferase ribozyme / ribozyme
Function / homologyGUANINE / THALLIUM (I) ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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: RNA 1
B: RNA 2
C: RNA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,05315
Polymers19,8343
Non-polymers2,21912
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-69 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.983, 71.983, 84.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain RNA 1 /


Mass: 4436.710 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, 12 molecules

#4: Chemical
ChemComp-TL / THALLIUM (I) ION / Thallium


Mass: 204.383 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Tl
#5: Chemical ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 36-42% MPD, 50mM MES (pH 6.5), 10mM sodium acetate, 100mM lithium acetate, 10mM magnesium acetate, 25mM thallium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9751 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9751 Å / Relative weight: 1
ReflectionResolution: 2.95→43.59 Å / Num. obs: 5037 / % possible obs: 99.9 % / Redundancy: 24.9 % / Biso Wilson estimate: 118.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 18.01
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 26.7 % / Mean I/σ(I) obs: 0.81 / Num. unique obs: 487 / CC1/2: 0.366 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q7X

7q7x


Resolution: 2.95→43.59 Å / SU ML: 0.3924 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.1485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2248 468 5.24 %
Rwork0.2092 8460 -
obs0.21 5037 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 123.94 Å2
Refinement stepCycle: LAST / Resolution: 2.95→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1312 22 0 1334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011477
X-RAY DIFFRACTIONf_angle_d0.312295
X-RAY DIFFRACTIONf_chiral_restr0.0167306
X-RAY DIFFRACTIONf_plane_restr0.001163
X-RAY DIFFRACTIONf_dihedral_angle_d12.3737724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.380.38131510.31832834X-RAY DIFFRACTION99.9
3.38-4.250.32551580.27792820X-RAY DIFFRACTION99.97
4.26-43.590.18031590.17412806X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: 46.0646783124 Å / Origin y: 13.5021787497 Å / Origin z: 42.8249597586 Å
111213212223313233
T0.779796032173 Å20.10522074896 Å20.0261799227791 Å2-0.695435395997 Å20.0542545445829 Å2--0.727784641811 Å2
L6.54147318052 °23.89382836863 °2-0.903103833203 °2-3.92791642075 °2-1.32107601128 °2--3.36306047505 °2
S0.432918043996 Å °-0.0643127756804 Å °0.00358361653766 Å °0.128503423324 Å °-0.382414068448 Å °-0.268978883696 Å °-0.139487956072 Å °0.625749793597 Å °-0.00824644564304 Å °
Refinement TLS groupSelection details: all

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