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- PDB-3mb5: Crystal structure of P. abyssi tRNA m1A58 methyltransferase in co... -

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Basic information

Entry
Database: PDB / ID: 3mb5
TitleCrystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-methionine
ComponentsSAM-dependent methyltransferase
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
ACETATE ION / S-ADENOSYLMETHIONINE / 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: 1.6 Å
AuthorsGuelorget, A. / Golinelli-Pimpaneau, B.
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
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,37713
Polymers29,1631
Non-polymers1,21412
Water6,125340
1
A: SAM-dependent methyltransferase
hetero molecules

A: SAM-dependent methyltransferase
hetero molecules

A: SAM-dependent methyltransferase
hetero molecules

A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,50852
Polymers116,6524
Non-polymers4,85748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area21520 Å2
ΔGint-149 kcal/mol
Surface area41320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.550, 89.260, 110.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SAM-dependent methyltransferase


Mass: 29162.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Gene: PAB0283, pimT-like, PYRAB04300 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q9V1J7, EC: 2.1.1.36

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Non-polymers , 5 types, 352 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.65 Å3/Da / Density % sol: 66.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.8M ammonium sulfate, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2010 / Details: bi-morph mirrors
RadiationMonochromator: cryogenically cooled monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 56562 / % possible obs: 99.8 % / Redundancy: 9.1 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 16.42
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 5.1 / Num. unique all: 9295 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 3LGA

3lga


Resolution: 1.6→19.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.298 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19891 2824 5 %RANDOM
Rwork0.18397 ---
obs0.18473 53652 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.151 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2--0.3 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 75 340 2469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222164
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9982910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22922.88797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61115386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2941519
X-RAY DIFFRACTIONr_chiral_restr0.0940.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211589
X-RAY DIFFRACTIONr_mcbond_it0.8231.51275
X-RAY DIFFRACTIONr_mcangle_it1.53822063
X-RAY DIFFRACTIONr_scbond_it2.5053889
X-RAY DIFFRACTIONr_scangle_it4.2144.5847
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 203 -
Rwork0.303 3866 -
obs-3866 100 %

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