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- PDB-5hjk: Crystal Structure of Pyrococcus abyssi Trm5a complexed with SAH -

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Basic information

Entry
Database: PDB / ID: 5hjk
TitleCrystal Structure of Pyrococcus abyssi Trm5a complexed with SAH
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
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine(37)-N(1))/4-demethylwyosine(37)-methyltransferase Taw22
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,1432
Polymers40,7591
Non-polymers3841
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19510 Å2
Unit cell
Length a, b, c (Å)52.852, 54.523, 129.968
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
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: BL19U1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 26250 / % possible obs: 100 % / Observed criterion σ(I): 5.3 / Redundancy: 12.5 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 18.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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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: 3AY0

3ay0


Resolution: 2→26.426 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.74
RfactorNum. reflection% reflection
Rfree0.2173 1331 5.09 %
Rwork0.1748 --
obs0.177 26146 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→26.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 26 257 3094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072893
X-RAY DIFFRACTIONf_angle_d1.1953906
X-RAY DIFFRACTIONf_dihedral_angle_d13.5431117
X-RAY DIFFRACTIONf_chiral_restr0.046445
X-RAY DIFFRACTIONf_plane_restr0.005496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9974-2.06880.30281200.2132404X-RAY DIFFRACTION98
2.0688-2.15160.23951300.19942445X-RAY DIFFRACTION100
2.1516-2.24940.22881310.18242444X-RAY DIFFRACTION100
2.2494-2.3680.24941220.18612470X-RAY DIFFRACTION100
2.368-2.51620.2821260.18992475X-RAY DIFFRACTION100
2.5162-2.71030.23611420.18892459X-RAY DIFFRACTION100
2.7103-2.98270.21671310.18912470X-RAY DIFFRACTION100
2.9827-3.41350.20671420.18312501X-RAY DIFFRACTION100
3.4135-4.29770.1951520.15312513X-RAY DIFFRACTION100
4.2977-26.42830.19481350.1592634X-RAY DIFFRACTION99

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