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- PDB-6qh8: Structure of knotted YibK from P. aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6qh8
TitleStructure of knotted YibK from P. aeruginosa
ComponentstRNA (cytidine(34)-2'-O)-methyltransferase
KeywordsTRANSFERASE / methyltransferase / topological knot / cyclized protein
Function / homology
Function and homology information


wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / RNA binding / cytoplasm
Similarity search - Function
tRNA (cytidine/uridine-2'-O-)-methyltransferase / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / tRNA (cytidine(34)-2'-O)-methyltransferase / tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMikula, K.M. / Tascon, I. / Iwai, H.
Funding support Finland, 2items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
Academy of Finland131413, 137995, 277335 Finland
CitationJournal: Front Chem / Year: 2021
Title: Tying up the Loose Ends: A Mathematically Knotted Protein.
Authors: Hsu, S.D. / Lee, Y.C. / Mikula, K.M. / Backlund, S.M. / Tascon, I. / Goldman, A. / Iwai, H.
History
DepositionJan 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (cytidine(34)-2'-O)-methyltransferase
B: tRNA (cytidine(34)-2'-O)-methyltransferase
C: tRNA (cytidine(34)-2'-O)-methyltransferase
D: tRNA (cytidine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,57023
Polymers72,7154
Non-polymers1,85519
Water2,954164
1
A: tRNA (cytidine(34)-2'-O)-methyltransferase
C: tRNA (cytidine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,31812
Polymers36,3582
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-149 kcal/mol
Surface area14490 Å2
MethodPISA
2
B: tRNA (cytidine(34)-2'-O)-methyltransferase
D: tRNA (cytidine(34)-2'-O)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,25211
Polymers36,3582
Non-polymers8959
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-97 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.932, 85.726, 167.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
tRNA (cytidine(34)-2'-O)-methyltransferase / tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL


Mass: 18178.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: trmL, C0043_37455, C0044_37955, C0046_35255, C8257_31370, CW299_37860, DN070_18550, PAMH19_2880
Production host: Escherichia coli (E. coli)
References: UniProt: A0A071LCY6, UniProt: Q9HU57*PLUS, tRNA (cytidine34-2'-O)-methyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.3 M ammonium sulfate, 0.1 M MES buffer (pH 6.0), 25% polyethylene glycol monomethyl ether (PEG MME) 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→28.17 Å / Num. obs: 36646 / % possible obs: 99.5 % / Redundancy: 13.1 % / Rrim(I) all: 0.134 / Net I/σ(I): 15.4
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2.24 / Num. unique obs: 5693 / % possible all: 97.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mxi

1mxi


Resolution: 2.2→28.167 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 1856 5.07 %RANDOM
Rwork0.1851 ---
obs0.1877 36635 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 101 164 5201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025134
X-RAY DIFFRACTIONf_angle_d1.586942
X-RAY DIFFRACTIONf_dihedral_angle_d7.7033040
X-RAY DIFFRACTIONf_chiral_restr0.061722
X-RAY DIFFRACTIONf_plane_restr0.011912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1959-2.25520.42041320.36852531X-RAY DIFFRACTION95
2.2552-2.32160.28021290.25882664X-RAY DIFFRACTION100
2.3216-2.39650.25841450.20032615X-RAY DIFFRACTION100
2.3965-2.48210.25751410.18482635X-RAY DIFFRACTION100
2.4821-2.58140.23651300.18082689X-RAY DIFFRACTION100
2.5814-2.69880.26831120.1862665X-RAY DIFFRACTION100
2.6988-2.84090.24491420.19762659X-RAY DIFFRACTION100
2.8409-3.01870.27371580.19482655X-RAY DIFFRACTION100
3.0187-3.25150.26051550.19262673X-RAY DIFFRACTION100
3.2515-3.57810.22341590.18122664X-RAY DIFFRACTION100
3.5781-4.09450.23141480.16252721X-RAY DIFFRACTION100
4.0945-5.15350.19651570.14962720X-RAY DIFFRACTION100
5.1535-28.1690.21281480.19112888X-RAY DIFFRACTION100

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