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- PDB-5wt1: Pyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cogn... -

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Basic information

Entry
Database: PDB / ID: 5wt1
TitlePyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cognate tRNA
Components
  • RNA (76-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 N1-guanine methylation / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasm
Similarity search - Function
tRNA methyltransferase 5, N-terminal / tRNA methyltransferase 5 N-terminal domain / : / : / TYW2 N-terminal domain / SAM-dependent methyltransferase TRM5/TYW2-type / SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / TRM5/TYW2 methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / : / RNA / RNA (> 10) / tRNA (guanine(37)-N(1))/4-demethylwyosine(37)-methyltransferase Taw22
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsXie, W. / Wang, C. / Jia, Q.
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 (76-MER)
B: tRNA (guanine(37)-N1)-methyltransferase Trm5a
F: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9626
Polymers126,1934
Non-polymers7692
Water1,08160
1
A: tRNA (guanine(37)-N1)-methyltransferase Trm5a
C: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4813
Polymers63,0972
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-32 kcal/mol
Surface area23250 Å2
MethodPISA
2
B: tRNA (guanine(37)-N1)-methyltransferase Trm5a
F: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4813
Polymers63,0972
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-30 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.096, 57.017, 115.807
Angle α, β, γ (deg.)90.00, 101.53, 90.00
Int Tables number3
Space group name H-MP121

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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.: 2
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 (76-MER)


Mass: 24551.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi GE5 (archaea) / References: GenBank: HE613800.1
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.62 Å3/Da / Density % sol: 53 %
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: BL17U / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.598→50 Å / Num. obs: 40587 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.911 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.739 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZZN

2zzn


Resolution: 2.598→40.217 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 2020 5.01 %
Rwork0.2474 --
obs0.2488 40281 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.598→40.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4966 2895 52 60 7973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058348
X-RAY DIFFRACTIONf_angle_d0.97612002
X-RAY DIFFRACTIONf_dihedral_angle_d14.9134706
X-RAY DIFFRACTIONf_chiral_restr0.0561491
X-RAY DIFFRACTIONf_plane_restr0.0071040
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5978-2.66280.45341470.38092484X-RAY DIFFRACTION92
2.6628-2.73470.41751210.35072769X-RAY DIFFRACTION100
2.7347-2.81520.38591290.34492749X-RAY DIFFRACTION100
2.8152-2.9060.38811430.34882748X-RAY DIFFRACTION100
2.906-3.00990.36331740.31342740X-RAY DIFFRACTION100
3.0099-3.13030.36611390.3052734X-RAY DIFFRACTION100
3.1303-3.27270.30961290.2692708X-RAY DIFFRACTION99
3.2727-3.44520.2771510.26132737X-RAY DIFFRACTION99
3.4452-3.66090.28211660.26032739X-RAY DIFFRACTION100
3.6609-3.94330.27571500.23492746X-RAY DIFFRACTION100
3.9433-4.33980.23341370.22262783X-RAY DIFFRACTION100
4.3398-4.96670.21641380.2122766X-RAY DIFFRACTION99
4.9667-6.25380.23511420.2252800X-RAY DIFFRACTION100
6.2538-40.22180.24351540.21152758X-RAY DIFFRACTION96

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