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- PDB-7nzj: Structure of bsTrmB apo -

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Basic information

Entry
Database: PDB / ID: 7nzj
TitleStructure of bsTrmB apo
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
tRNA (guanine-N(7)-)-methyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 24, 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (guanine-N(7)-)-methyltransferase
B: tRNA (guanine-N(7)-)-methyltransferase
C: tRNA (guanine-N(7)-)-methyltransferase
D: tRNA (guanine-N(7)-)-methyltransferase
E: tRNA (guanine-N(7)-)-methyltransferase
F: tRNA (guanine-N(7)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,71012
Polymers147,2266
Non-polymers4836
Water16,430912
1
A: tRNA (guanine-N(7)-)-methyltransferase
B: tRNA (guanine-N(7)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1914
Polymers49,0752
Non-polymers1152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-14 kcal/mol
Surface area19090 Å2
MethodPISA
2
C: tRNA (guanine-N(7)-)-methyltransferase
D: tRNA (guanine-N(7)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3525
Polymers49,0752
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-6 kcal/mol
Surface area18780 Å2
MethodPISA
3
E: tRNA (guanine-N(7)-)-methyltransferase
F: tRNA (guanine-N(7)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1683
Polymers49,0752
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-6 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.620, 103.680, 103.690
Angle α, β, γ (deg.)118.120, 97.910, 97.840
Int Tables number1
Space group name H-MP1

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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.: 6
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 912 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2M NaCl, 0.1M MES, 15% v/v 5/4PO/OH,

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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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.98→44.53 Å / Num. obs: 96395 / % possible obs: 91.5 % / Redundancy: 3.861 % / Biso Wilson estimate: 42.408 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.083 / Χ2: 0.85 / Net I/σ(I): 12.47 / Num. measured all: 372163 / Scaling rejects: 51
Reflection shellResolution: 1.98→2 Å / Redundancy: 3.896 % / Rmerge(I) obs: 1.344 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 2799 / CC1/2: 0.548 / Rrim(I) all: 1.557 / % possible all: 89.9

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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: 1.98→44.53 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2146 / WRfactor Rwork: 0.1808 / FOM work R set: 0.7547 / SU B: 5.5 / SU ML: 0.142 / SU R Cruickshank DPI: 0.1853 / SU Rfree: 0.1594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 5048 5.2 %RANDOM
Rwork0.1874 ---
obs0.1893 91357 91.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.52 Å2 / Biso mean: 41.456 Å2 / Biso min: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å2-0.47 Å2-0.36 Å2
2---1.71 Å20.31 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.98→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9925 0 31 912 10868
Biso mean--55.27 48.42 -
Num. residues----1228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310182
X-RAY DIFFRACTIONr_bond_other_d0.0350.0179503
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.64213749
X-RAY DIFFRACTIONr_angle_other_deg2.2321.58721941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21751222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09623.768552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.695151788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9531542
X-RAY DIFFRACTIONr_chiral_restr0.070.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211572
X-RAY DIFFRACTIONr_gen_planes_other0.010.022368
LS refinement shellResolution: 1.98→2.031 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 315 -
Rwork0.341 6866 -
all-7181 -
obs--90.47 %

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