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- PDB-6q56: Crystal structure of the B. subtilis M1A22 tRNA methyltransferase TrmK -

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Basic information

Entry
Database: PDB / ID: 6q56
TitleCrystal structure of the B. subtilis M1A22 tRNA methyltransferase TrmK
ComponentstRNA (adenine(22)-N(1))-methyltransferase
KeywordsRNA BINDING PROTEIN / methyltransferase / tRNA methyltransferase
Function / homology
Function and homology information


tRNA (adenine22-N1)-methyltransferase / tRNA (adenine(22)-N1)-methyltransferase activity / tRNA processing / methylation / cytoplasm
Similarity search - Function
tRNA methyltransferase TrmK / tRNA (adenine(22)-N(1))-methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / tRNA (adenine(22)-N(1))-methyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDegut, C. / Roovers, M. / Barraud, P. / Brachet, F. / Feller, A. / Larue, V. / Al Refaii, A. / Caillet, J. / Droogmans, L. / Tisne, C.
Citation
Journal: Nucleic Acids Res. / Year: 2019
Title: Structural characterization of B. subtilis m1A22 tRNA methyltransferase TrmK: insights into tRNA recognition.
Authors: Degut, C. / Roovers, M. / Barraud, P. / Brachet, F. / Feller, A. / Larue, V. / Al Refaii, A. / Caillet, J. / Droogmans, L. / Tisne, C.
#1: Journal: Biomol NMR Assign / Year: 2016
Title: Backbone resonance assignments of the m1A22 tRNA methyltransferase TrmK from Bacillus subtilis.
Authors: Degut, C. / Barraud, P. / Larue, V. / Tisne, C.
History
DepositionDec 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 22, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (adenine(22)-N(1))-methyltransferase
B: tRNA (adenine(22)-N(1))-methyltransferase
C: tRNA (adenine(22)-N(1))-methyltransferase
D: tRNA (adenine(22)-N(1))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8988
Polymers104,6634
Non-polymers2354
Water5,459303
1
A: tRNA (adenine(22)-N(1))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2242
Polymers26,1661
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA (adenine(22)-N(1))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2242
Polymers26,1661
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: tRNA (adenine(22)-N(1))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2242
Polymers26,1661
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: tRNA (adenine(22)-N(1))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2242
Polymers26,1661
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.560, 51.980, 108.130
Angle α, β, γ (deg.)90.00, 110.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
tRNA (adenine(22)-N(1))-methyltransferase / TrMet(m1A22) / tRNA(m1A22)-methyltransferase / tRNA(m1A22)MTase


Mass: 26165.803 Da / Num. of mol.: 4 / Mutation: C35S C152S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: trmK, yqfN, BSU25180 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P54471, tRNA (adenine22-N1)-methyltransferase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M ammonium acetate 0.1 M sodium acetate trihydrate pH 5 30% w/v polyethylene glycol 4000 8% 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.98→46.24 Å / Num. obs: 57747 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.71 Å2 / Rmerge(I) obs: 0.2108 / Net I/σ(I): 12
Reflection shellResolution: 1.98→2.175 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.451 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 4968 / CC1/2: 0.227 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KU1

3ku1


Resolution: 2→46.239 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 2884 5 %
Rwork0.2123 --
obs0.2136 57657 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→46.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7232 0 4 303 7539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0327353
X-RAY DIFFRACTIONf_angle_d1.29884
X-RAY DIFFRACTIONf_dihedral_angle_d13.6797936
X-RAY DIFFRACTIONf_chiral_restr0.0791120
X-RAY DIFFRACTIONf_plane_restr0.0041276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03280.41421340.37682549X-RAY DIFFRACTION100
2.0328-2.06780.41441370.37752595X-RAY DIFFRACTION100
2.0678-2.10540.38851360.35672576X-RAY DIFFRACTION100
2.1054-2.14590.36881360.35422598X-RAY DIFFRACTION100
2.1459-2.18970.40931350.34672562X-RAY DIFFRACTION100
2.1897-2.23740.35621370.32862601X-RAY DIFFRACTION100
2.2374-2.28940.32191360.29212585X-RAY DIFFRACTION100
2.2894-2.34670.29571380.26492634X-RAY DIFFRACTION100
2.3467-2.41010.29131360.24122569X-RAY DIFFRACTION100
2.4101-2.4810.26091380.23272630X-RAY DIFFRACTION100
2.481-2.56110.24061350.22522566X-RAY DIFFRACTION100
2.5611-2.65260.2761360.2262585X-RAY DIFFRACTION100
2.6526-2.75880.27351390.22312633X-RAY DIFFRACTION100
2.7588-2.88430.27841370.22082601X-RAY DIFFRACTION100
2.8843-3.03640.2421370.21432616X-RAY DIFFRACTION100
3.0364-3.22660.2271390.20542623X-RAY DIFFRACTION100
3.2266-3.47560.21291370.20052614X-RAY DIFFRACTION100
3.4756-3.82530.20851380.1742613X-RAY DIFFRACTION100
3.8253-4.37840.17561390.15312638X-RAY DIFFRACTION100
4.3784-5.51490.17591400.15492661X-RAY DIFFRACTION100
5.5149-46.25130.16591440.182724X-RAY DIFFRACTION99

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