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- PDB-5wt3: Pyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cogn... -

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Basic information

Entry
Database: PDB / ID: 5wt3
TitlePyrococcus abyssi methyltransferase PaTrm5a bound by MTA and cognate tRNA
Components
  • RNA (73-MER)
  • tRNA (guanine(37)-N1)-methyltransferase Trm5a
KeywordsTRANSFERASE/RNA / methyltransferase / Trm5a / wyosine hypermodification / TRANSFERASE-RNA complex
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasm
Similarity search - Function
SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / SAM-dependent methyltransferase TRM5/TYW2-type / Met-10+ like-protein / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / : / RNA / RNA (> 10) / tRNA (guanine(37)-N1)/4-demethylwyosine(37)-methyltransferase Taw22
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.204 Å
AuthorsXie, W. / Wang, C. / Jia, Q.
Funding support China, 2items
OrganizationGrant numberCountry
Fundamental Research Funds for the Central Universities16lgjc76 China
the Science and Technology Program of Guangzhou201504010025 China
CitationJournal: Sci Adv / Year: 2017
Title: Structural insight into the methyltransfer mechanism of the bifunctional Trm5.
Authors: Wang, C. / Jia, Q. / Zeng, J. / Chen, R. / Xie, W.
History
DepositionDec 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 8, 2023Group: 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 (guanine(37)-N1)-methyltransferase Trm5a
C: RNA (73-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3943
Polymers63,0972
Non-polymers2971
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-27 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.069, 212.302, 130.035
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 (guanine(37)-N1)-methyltransferase Trm5a / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 38545.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: trm5a, PYRAB01130, PAB2272 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9V2G1, tRNA (guanine37-N1)-methyltransferase
#2: RNA chain RNA (73-MER)


Mass: 24551.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi GE5 (archaea) / References: GenBank: HE613800.1
#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.18 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 45% MPD, 100 mM MES (pH 6.5), 200 mM NH4OAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CCD / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 13684 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 18.9
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 8.5 / CC1/2: 0.995 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZZN

2zzn


Resolution: 3.204→49.14 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 667 4.95 %
Rwork0.2469 --
obs0.2475 13477 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.204→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 1565 20 13 3866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054085
X-RAY DIFFRACTIONf_angle_d0.945935
X-RAY DIFFRACTIONf_dihedral_angle_d14.5372243
X-RAY DIFFRACTIONf_chiral_restr0.054740
X-RAY DIFFRACTIONf_plane_restr0.006507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2035-3.45080.35891460.29962408X-RAY DIFFRACTION95
3.4508-3.7980.34391370.26462511X-RAY DIFFRACTION99
3.798-4.34730.22021130.2512583X-RAY DIFFRACTION100
4.3473-5.4760.25721290.25962603X-RAY DIFFRACTION100
5.476-49.14560.23331420.22542705X-RAY DIFFRACTION100

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