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- PDB-6qkv: Structure of YibK from P. aeruginosa -

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Basic information

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


wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (cytidine(34)-2'-O)-methyltransferase activity / tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity / tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / RNA binding / identical protein 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
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 / Resolution: 2.01 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 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,44913
Polymers35,4122
Non-polymers1,03711
Water2,792155
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-99 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.661, 167.114, 48.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 17706.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: trmL, C0044_37955, C8257_31370, DZ962_17365, 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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M ammonium sulfate, 0.9 M lithium sulfate, 0.1 M sodium citrate buffer, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.01→46.7 Å / Num. obs: 23919 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rrim(I) all: 0.071 / Net I/σ(I): 18.52
Reflection shellResolution: 2.01→2.13 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.84 / Num. unique obs: 3813 / Rrim(I) all: 0.665 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mxi

1mxi


Resolution: 2.01→46.699 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.45
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 2000 8.36 %RANDOM
Rwork0.1918 ---
obs0.1953 23910 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.01→46.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 60 155 2491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082382
X-RAY DIFFRACTIONf_angle_d0.9693221
X-RAY DIFFRACTIONf_dihedral_angle_d4.0941406
X-RAY DIFFRACTIONf_chiral_restr0.054337
X-RAY DIFFRACTIONf_plane_restr0.007419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0059-2.05610.30461400.28441535X-RAY DIFFRACTION99
2.0561-2.11170.28761410.26081541X-RAY DIFFRACTION99
2.1117-2.17380.25751390.21641527X-RAY DIFFRACTION100
2.1738-2.2440.25951420.22761552X-RAY DIFFRACTION100
2.244-2.32420.27221420.22851546X-RAY DIFFRACTION99
2.3242-2.41730.24091410.19671552X-RAY DIFFRACTION100
2.4173-2.52730.24311410.19581551X-RAY DIFFRACTION100
2.5273-2.66050.25941420.20381551X-RAY DIFFRACTION100
2.6605-2.82720.25991430.20041562X-RAY DIFFRACTION100
2.8272-3.04540.25931420.20671572X-RAY DIFFRACTION100
3.0454-3.35180.20551450.18781578X-RAY DIFFRACTION100
3.3518-3.83660.20821430.16291569X-RAY DIFFRACTION99
3.8366-4.83290.1931470.1621612X-RAY DIFFRACTION99
4.8329-46.71160.25281520.19271662X-RAY DIFFRACTION98

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