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- PDB-3lhd: Crystal structure of P. abyssi tRNA m1A58 methyltransferase in co... -

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Basic information

Entry
Database: PDB / ID: 3lhd
TitleCrystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-homocysteine
ComponentsSAM-dependent methyltransferase, putative
KeywordsTRANSFERASE / RNA methyltransferase / m1A / TrmI / intermolecular contacts / region-specificity / tetramer / disulfide bond / hyperthermostability / Methyltransferase
Function / homology
Function and homology information


tRNA (adenine57-N1/adenine58-N1)-methyltransferase / tRNA (adenine(57)-N1)/(adenine(58)-N1)-methyltransferase activity / tRNA (m1A) methyltransferase complex / tRNA (adenine(58)-N1)-methyltransferase activity / tRNA methylation
Similarity search - Function
TrmI-like N-terminal / Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / : / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll ...TrmI-like N-terminal / Vcp-like ATPase; Chain A, domain 2 - #20 / tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14 / : / tRNA methyltransferase complex GCD14 subunit / tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile. / Vcp-like ATPase; Chain A, domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsGuelorget, A. / Golinelli-Pimpaneau, B. / Wouters, J. / Barbey, C.
Citation
Journal: Nucleic Acids Res. / Year: 2010
Title: Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase.
Authors: Guelorget, A. / Roovers, M. / Guerineau, V. / Barbey, C. / Li, X. / Golinelli-Pimpaneau, B.
#1: Journal: Nucleic Acids Res. / Year: 2004
Title: A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase
Authors: Roovers, M. / Wouters, J. / Bujnicki, J.M. / Tricot, C. / Stalon, V. / Grosjean, H. / Droogmans, L.
History
DepositionJan 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: SAM-dependent methyltransferase, putative
A: SAM-dependent methyltransferase, putative
B: SAM-dependent methyltransferase, putative
D: SAM-dependent methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2208
Polymers115,6834
Non-polymers1,5384
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-94 kcal/mol
Surface area40190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.030, 127.577, 151.396
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
SAM-dependent methyltransferase, putative


Mass: 28920.662 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Gene: PAB0283 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q9V1J7, EC: 2.1.1.36
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M ammonium sulfate, 0.1M sodium acetate, 25% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.59→65.1 Å / Num. all: 38766 / Num. obs: 38327 / % possible obs: 94.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.7
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 2.4 / % possible all: 68.6

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I9G

1i9g


Resolution: 2.59→58.78 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.874 / SU B: 12.242 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.932 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28614 1908 5 %RANDOM
Rwork0.23059 ---
obs0.23335 36361 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.8 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.59→58.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7950 0 104 131 8185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228242
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.97411175
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20651008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71722.609368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.879151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.311574
X-RAY DIFFRACTIONr_chiral_restr0.0820.21249
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216242
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.23720
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.25420
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2355
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4941.55051
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95128131
X-RAY DIFFRACTIONr_scbond_it1.22533191
X-RAY DIFFRACTIONr_scangle_it2.1834.53044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.592→2.659 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 86 -
Rwork0.333 1433 -
obs--50.97 %

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