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- PDB-5hji: Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine -

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Basic information

Entry
Database: PDB / ID: 5hji
TitleCrystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine
ComponentstRNA (guanine(37)-N1)-methyltransferase Trm5a
KeywordsTRANSFERASE / Methyltransferase / Trm5a / SAM / Adenosine / tRNA modification
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 / Met-10+ protein-like domains / : / : / TYW2 N-terminal domain / SAM-dependent methyltransferase TRM5/TYW2-type / SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / TRM5/TYW2 methyltransferase domain / GMP Synthetase; Chain A, domain 3 ...tRNA methyltransferase 5, N-terminal / tRNA methyltransferase 5 N-terminal domain / Met-10+ protein-like domains / : / : / TYW2 N-terminal domain / SAM-dependent methyltransferase TRM5/TYW2-type / SAM-dependent methyltransferase TRM5/TYW2-type domain profile. / TRM5/TYW2 methyltransferase domain / GMP Synthetase; Chain A, domain 3 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / tRNA (guanine(37)-N(1))/4-demethylwyosine(37)-methyltransferase Taw22
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXie, W. / Wang, C. / Jia, Q.
Funding support China, 3items
OrganizationGrant numberCountry
Guangdong Innovative Research Team2011Y038 China
Science and Technology Program of Guangzhou201504010025 China
Fundamental Research Funds for the Central Universities15lgjc02 China
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structures of the bifunctional tRNA methyltransferase Trm5a
Authors: Wang, C. / Jia, Q. / Chen, R. / Wei, Y. / Li, J. / Ma, J. / Xie, W.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (guanine(37)-N1)-methyltransferase Trm5a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0262
Polymers40,7591
Non-polymers2671
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint2 kcal/mol
Surface area19570 Å2
Unit cell
Length a, b, c (Å)52.727, 54.718, 128.948
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 (guanine(37)-N1)-methyltransferase Trm5a / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 40758.512 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 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9V2G1, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10-15% PEG3350, 100mM HEPES, pH7.5, 100mM Ca(OAc)2 and 100mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Nov 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.2→24.574 Å / Num. obs: 19382 / % possible obs: 99.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HJK

5hjk


Resolution: 2.2→24.574 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.72
RfactorNum. reflection% reflection
Rfree0.2361 991 5.12 %
Rwork0.1932 --
obs0.1954 19348 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 19 243 3092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032907
X-RAY DIFFRACTIONf_angle_d0.8093927
X-RAY DIFFRACTIONf_dihedral_angle_d11.6481113
X-RAY DIFFRACTIONf_chiral_restr0.027445
X-RAY DIFFRACTIONf_plane_restr0.003501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.3160.31791500.2492555X-RAY DIFFRACTION99
2.316-2.4610.31051550.23392577X-RAY DIFFRACTION99
2.461-2.65080.27031360.22652625X-RAY DIFFRACTION100
2.6508-2.91710.25651390.22092631X-RAY DIFFRACTION100
2.9171-3.33830.27541470.20262641X-RAY DIFFRACTION100
3.3383-4.20250.19141360.16492673X-RAY DIFFRACTION99
4.2025-24.57560.17241280.15672655X-RAY DIFFRACTION94

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