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- PDB-7q7z: Crystal structure of the methyltransferase-ribozyme 1 (with 1-ben... -

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Basic information

Entry
Database: PDB / ID: 7q7z
TitleCrystal structure of the methyltransferase-ribozyme 1 (with 1-benzylamine-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: 3.26 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)40,25611
Polymers39,8806
Non-polymers3755
Water1086
1
A: RNA 1
B: RNA 2
C: RNA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1406
Polymers19,9403
Non-polymers2003
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-8 kcal/mol
Surface area10570 Å2
MethodPISA
2
D: RNA 1
E: RNA 2
F: RNA 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1165
Polymers19,9403
Non-polymers1752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-8 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.861, 117.861, 83.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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RNA chain , 3 types, 6 molecules ADBECF

#1: RNA chain RNA 1


Mass: 4542.855 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 / Details: GCUGGGACAACUAGACAUACAGUG / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 11 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O
#6: 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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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: 3.63 Å3/Da / Density % sol: 66.07 %
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: 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: 3.26→44.54 Å / Num. obs: 9584 / % possible obs: 99.71 % / Redundancy: 15.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.9
Reflection shellResolution: 3.26→3.38 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 937 / CC1/2: 0.236 / % possible all: 98.83

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Processing

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

7q7x


Resolution: 3.26→44.54 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 521 5.45 %
Rwork0.2102 --
obs0.2132 9568 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.26→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2640 24 6 2670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012978
X-RAY DIFFRACTIONf_angle_d0.3034629
X-RAY DIFFRACTIONf_dihedral_angle_d13.0611470
X-RAY DIFFRACTIONf_chiral_restr0.011612
X-RAY DIFFRACTIONf_plane_restr0.001128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.26-3.590.39271290.35242195X-RAY DIFFRACTION99
3.59-4.110.27961250.27012218X-RAY DIFFRACTION100
4.11-5.180.27881250.25882260X-RAY DIFFRACTION100
5.18-44.540.24231420.16932374X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.4042 Å / Origin y: -41.2435 Å / Origin z: -8.9227 Å
111213212223313233
T0.8298 Å2-0.0257 Å2-0.0935 Å2-0.7939 Å20.043 Å2--1.1314 Å2
L3.3175 °2-1.5612 °21.0985 °2-4.5979 °2-1.5586 °2--2.878 °2
S0.3016 Å °0.1664 Å °-0.5917 Å °-0.3397 Å °-0.086 Å °0.5508 Å °-0.0483 Å °-0.0941 Å °-0.2191 Å °
Refinement TLS groupSelection details: all

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