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- PDB-7q80: Crystal structure of the methyltransferase-ribozyme 1, no Magnesi... -

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Basic information

Entry
Database: PDB / ID: 7q80
TitleCrystal structure of the methyltransferase-ribozyme 1, no Magnesium condition (with 1-methyl-adenosine)
Components
  • RNA 1
  • RNA 2
  • RNA 3
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: 3.14 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
D: RNA 1
E: RNA 2
F: RNA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9939
Polymers39,6686
Non-polymers3253
Water00
1
A: RNA 1
B: RNA 2
C: RNA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0085
Polymers19,8343
Non-polymers1742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-11 kcal/mol
Surface area10480 Å2
MethodPISA
2
D: RNA 1
E: RNA 2
F: RNA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9854
Polymers19,8343
Non-polymers1511
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint3 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.867, 120.867, 82.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4

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Components

#1: RNA chain RNA 1


Mass: 4436.710 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA 2


Mass: 7641.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA 3


Mass: 7755.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O
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: 3.79 Å3/Da / Density % sol: 67.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 36-42% MPD, 50mM MES pH 6.4-6.7, 100mM NaCl, 100mM LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.15→45.17 Å / Num. obs: 11036 / % possible obs: 99.1 % / Redundancy: 25.3 % / Biso Wilson estimate: 126.52 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.52
Reflection shellResolution: 3.15→3.26 Å / Mean I/σ(I) obs: 0.56 / Num. unique obs: 1054 / CC1/2: 0.258

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Processing

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

7q7x


Resolution: 3.14→45.17 Å / SU ML: 0.4418 / Cross valid method: FREE R-VALUE / σ(F): 0.58 / Phase error: 31.4466
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205 1015 5.03 %
Rwork0.1756 19160 -
obs0.177 20175 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 151.93 Å2
Refinement stepCycle: LAST / Resolution: 3.14→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2624 23 0 2647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012954
X-RAY DIFFRACTIONf_angle_d0.26334590
X-RAY DIFFRACTIONf_chiral_restr0.0147612
X-RAY DIFFRACTIONf_plane_restr0.0011126
X-RAY DIFFRACTIONf_dihedral_angle_d11.21311448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.310.37951620.35042572X-RAY DIFFRACTION94.67
3.31-3.510.3191350.29352780X-RAY DIFFRACTION100
3.51-3.780.29631730.2642729X-RAY DIFFRACTION100
3.79-4.170.24761210.23112809X-RAY DIFFRACTION100
4.17-4.770.27021330.20052748X-RAY DIFFRACTION100
4.77-60.22871470.17512754X-RAY DIFFRACTION99.97
6.01-45.170.13841440.12272768X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 20.7161107677 Å / Origin y: -42.4562497196 Å / Origin z: -8.96222318224 Å
111213212223313233
T0.822333321246 Å2-0.112334522766 Å20.0149596858747 Å2-0.830384066887 Å20.0806748741068 Å2--1.10667491909 Å2
L2.545292653 °2-0.778318435243 °20.886395736435 °2-3.7111039384 °2-0.544430095609 °2--2.37828275223 °2
S-0.149926006974 Å °0.317733843524 Å °0.104636445019 Å °0.0378178982757 Å °-0.00570184416081 Å °0.0301026470962 Å °-0.379068596158 Å °0.0858401280529 Å °0.143546698691 Å °
Refinement TLS groupSelection details: all

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