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- PDB-7nyb: TrmB complex with SAM -

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Basic information

Entry
Database: PDB / ID: 7nyb
TitleTrmB complex with SAM
ComponentstRNA (guanine-N(7)-)-methyltransferase
KeywordsRNA BINDING PROTEIN / m7G Methyltransferase / Rossman-like fold / tRNA modifying enzyme
Function / homology
Function and homology information


RNA (guanine-N7)-methylation / tRNA (guanine46-N7)-methyltransferase / tRNA (guanine(46)-N7)-methyltransferase activity / tRNA methyltransferase complex / tRNA methylation
Similarity search - Function
: / SAM-dependent methyltransferase TRMB-type domain profile. / tRNA (guanine-N-7) methyltransferase, Trmb type / Putative methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / tRNA (guanine-N(7)-)-methyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBlersch, K.F. / Ficner, R. / Neumann, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Rna Biol. / Year: 2021
Title: Structural model of the M7G46 Methyltransferase TrmB in complex with tRNA.
Authors: Blersch, K.F. / Burchert, J.P. / August, S.C. / Welp, L. / Neumann, P. / Koster, S. / Urlaub, H. / Ficner, R.
History
DepositionMar 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (guanine-N(7)-)-methyltransferase
B: tRNA (guanine-N(7)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8724
Polymers49,0752
Non-polymers7972
Water81145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.190, 178.190, 37.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 10 - 212 / Label seq-ID: 10 - 212

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.80399, 0.048835, 0.592635), (0.114339, -0.965329, 0.234663), (0.583547, 0.256427, 0.770531)56.219181, -9.56875, -17.2204

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Components

#1: Protein tRNA (guanine-N(7)-)-methyltransferase / BsTrmB / tRNA (guanine(46)-N(7))-methyltransferase / tRNA(m7G46)-methyltransferase


Mass: 24537.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: trmB, ytmQ, BSU29900 / Production host: Escherichia coli (E. coli)
References: UniProt: O34522, tRNA (guanine46-N7)-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20%PEG4000, 20%Glycerol, 0.06M KAc, 0.08M (NH4)2SO4, 0.01M Triethylamine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.45→44.55 Å / Num. obs: 16092 / % possible obs: 99.9 % / Redundancy: 10.551 % / Biso Wilson estimate: 64.066 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.113 / Χ2: 0.897 / Net I/σ(I): 13.31 / Num. measured all: 169792
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 10.808 % / Rmerge(I) obs: 1.307 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 939 / CC1/2: 0.746 / Rrim(I) all: 1.372 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FCA

2fca


Resolution: 2.5→44.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2552 / WRfactor Rwork: 0.2099 / FOM work R set: 0.7625 / SU B: 12.786 / SU ML: 0.271 / SU R Cruickshank DPI: 1.1482 / SU Rfree: 0.3146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.148 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 758 5 %RANDOM
Rwork0.2088 ---
obs0.2111 14395 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.69 Å2 / Biso mean: 66.423 Å2 / Biso min: 31.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-0.56 Å20 Å2
2---1.12 Å20 Å2
3---3.64 Å2
Refinement stepCycle: final / Resolution: 2.5→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 54 45 3416
Biso mean--86.42 53.62 -
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133453
X-RAY DIFFRACTIONr_bond_other_d0.0340.0173205
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.6464672
X-RAY DIFFRACTIONr_angle_other_deg2.2921.5897401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.455408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14723.784185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91215597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2191514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023922
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02800
Refine LS restraints NCSNumber: 1641 / Type: TIGHT THERMAL / Rms dev position: 9.66 Å / Weight position: 0.5
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 55 -
Rwork0.337 1051 -
all-1106 -
obs--100 %

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