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- PDB-5hjm: Crystal Structure of Pyrococcus abyssi Trm5a complexed with MTA -

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Basic information

Entry
Database: PDB / ID: 5hjm
TitleCrystal Structure of Pyrococcus abyssi Trm5a complexed with MTA
ComponentstRNA (guanine(37)-N1)-methyltransferase Trm5a
KeywordsTRANSFERASE / Methyltransferase / Trm5a / SAM / 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
ACETATE ION / HOMOSERINE LACTONE / 5'-DEOXY-5'-METHYLTHIOADENOSINE / tRNA (guanine(37)-N(1))/4-demethylwyosine(37)-methyltransferase Taw22
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.762 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)41,2164
Polymers40,7591
Non-polymers4573
Water7,350408
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-2 kcal/mol
Surface area19610 Å2
Unit cell
Length a, b, c (Å)52.969, 55.334, 130.376
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-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H15N5O3S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-HSL / HOMOSERINE LACTONE


Type: L-peptide linking / Mass: 101.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.57 Å3/Da / Density % sol: 47.88 %
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
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 38919 / % possible obs: 99.4 % / Observed criterion σ(I): 6.5 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.1
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 6.5 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HJK

5hjk


Resolution: 1.762→36.72 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.98
RfactorNum. reflection% reflection
Rfree0.2028 1880 4.87 %
Rwork0.1761 --
obs0.1775 38622 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.762→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 31 408 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042929
X-RAY DIFFRACTIONf_angle_d0.8973951
X-RAY DIFFRACTIONf_dihedral_angle_d13.1461134
X-RAY DIFFRACTIONf_chiral_restr0.035446
X-RAY DIFFRACTIONf_plane_restr0.003503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7616-1.80920.30121200.22112754X-RAY DIFFRACTION98
1.8092-1.86250.25421370.19812808X-RAY DIFFRACTION100
1.8625-1.92260.24821240.19282797X-RAY DIFFRACTION100
1.9226-1.99130.23521410.18942798X-RAY DIFFRACTION100
1.9913-2.0710.221400.18242806X-RAY DIFFRACTION100
2.071-2.16520.21391570.18272780X-RAY DIFFRACTION100
2.1652-2.27940.21121340.18312815X-RAY DIFFRACTION100
2.2794-2.42220.25831390.18852843X-RAY DIFFRACTION100
2.4222-2.60910.23081650.1862801X-RAY DIFFRACTION100
2.6091-2.87160.19241600.18282802X-RAY DIFFRACTION100
2.8716-3.28690.22361610.18162863X-RAY DIFFRACTION100
3.2869-4.14030.17331440.15912886X-RAY DIFFRACTION100
4.1403-36.72290.16171580.15942989X-RAY DIFFRACTION99

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