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- PDB-8fch: Apo Structure of (N1G37) Methyltransferase from Mycobacterium avium -

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Basic information

Entry
Database: PDB / ID: 8fch
TitleApo Structure of (N1G37) Methyltransferase from Mycobacterium avium
ComponentstRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase
KeywordsTRANSFERASE / TrmD / frameshift mutation
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytoplasm
Similarity search - Function
tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.956 Å
AuthorsIsaacson, B. / Brylewski, J. / Schlegel, F. / Cortes, J. / Lavallee, T. / Mehta, K. / Young, A. / Doti, L. / Battaile, K.P. / Stojanoff, V. ...Isaacson, B. / Brylewski, J. / Schlegel, F. / Cortes, J. / Lavallee, T. / Mehta, K. / Young, A. / Doti, L. / Battaile, K.P. / Stojanoff, V. / Perez, A. / Bolen, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Brookhaven National Laboratory (BNL)DE-SC0012704 United States
CitationJournal: To Be Published
Title: Apo structure of (N1G37) Methyltransferase from Mycobacterium avium.
Authors: Isaacson, B. / Brylewski, J. / Schlegel, F. / Cortes, J. / Lavallee, T. / Mehta, K. / Young, A. / Doti, L. / Battaile, K.P. / Stojanoff, V. / Perez, A. / Bolen, R.
History
DepositionDec 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (guanine-N(1)-)-methyltransferase
B: tRNA (guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)57,3032
Polymers57,3032
Non-polymers00
Water4,071226
1
A: tRNA (guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)28,6511
Polymers28,6511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA (guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)28,6511
Polymers28,6511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.2, 71.2, 240.405
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein tRNA (guanine-N(1)-)-methyltransferase / TRNA (guanine9-N1)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 28651.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Gene: trmD, MAP_2974c / Production host: Escherichia coli (E. coli)
References: UniProt: Q73VN9, tRNA (guanine37-N1)-methyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium sulfate, 0.1M bis-tris propane, pH 8.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.956→68.269 Å / Num. obs: 27639 / % possible obs: 92.5 % / Redundancy: 2.97 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.991 / CC1/2 anomalous: -0.057 / Rmerge(I) obs: 0.0917 / Rpim(I) all: 0.0627 / Rrim(I) all: 0.1116 / AbsDiff over sigma anomalous: 0.76 / Baniso tensor eigenvalue 1: 60.8 Å2 / Baniso tensor eigenvalue 2: 60.8 Å2 / Baniso tensor eigenvalue 3: 34 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 2.474 Å / Aniso diffraction limit 2: 2.474 Å / Aniso diffraction limit 3: 1.904 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 6.56 / Num. measured all: 82054 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 80.5 / % possible ellipsoidal: 92.5 / % possible ellipsoidal anomalous: 80.5 / % possible spherical: 60.2 / % possible spherical anomalous: 50.6 / Redundancy anomalous: 1.66 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
6.456-68.2692.880.062413.1339783978138213820.99-0.010.04240.07590.6696.694.496.694.496.61.7894.4
5.089-6.4563.040.069112.8242054205138213820.987-0.2020.04650.08360.71394.597.494.597.494.51.7697.4
4.409-5.0892.780.071312.3438353835138113810.986-0.1130.04880.08680.78781.894.581.894.581.81.6294.5
3.99-4.4092.640.073311.5236533653138213820.9860.1410.05220.09040.81283.796.483.796.483.71.596.4
3.698-3.992.710.080110.837503750138313830.981-0.3760.05680.09860.77680.397.580.397.580.31.5797.5
3.475-3.6982.890.085910.5739973997138113810.983-0.2260.05950.1050.79886.397.986.397.986.31.6197.9
3.3-3.4752.940.09988.7240724072138313830.98-0.0220.06880.12180.79786.99986.99986.91.6399
3.154-3.330.11397.9241454145138213820.981-0.0010.07790.13860.82487.698.987.698.987.61.6598.9
3.03-3.1543.030.14376.4741764176138013800.979-0.0160.09670.17390.83588.798.488.798.488.71.6798.4
2.924-3.033.060.15535.8942324232138313830.98-0.0850.10410.18770.7748998.98998.9891.6798.9
2.83-2.9243.080.1994.7742544254138213820.972-0.030.13380.24080.77788.898.688.898.688.81.6798.6
2.747-2.833.110.22444.2742954295138113810.9650.0480.14940.27070.78588.498.688.498.688.41.6998.6
2.674-2.7473.140.29513.5243404340138213820.941-0.0690.19610.35560.74589.298.689.298.689.21.7198.6
2.606-2.6743.150.31163.1643554355138213820.945-0.0610.20720.37560.73488.597.388.597.388.51.797.3
2.542-2.6063.210.35352.9444434443138213820.9460.0050.22970.42290.74683.493.383.493.383.41.7493.3
2.472-2.5423.180.36712.9143964396138213820.911-0.0280.23960.43980.73367.576.967.576.867.51.7476.9
2.391-2.4723.080.38522.7942534253138313830.892-0.0130.25710.46480.71865.17965.158.147.41.779
2.294-2.3913.020.41862.5641784178138213820.878-0.0750.280.50540.73466.183.766.142.532.71.6783.7
2.182-2.2942.860.48232.3239513951138213820.811-0.1830.32730.58520.70765.989.465.930.321.21.5889.4
1.956-2.1822.570.62531.735463546138213820.674-0.1110.43980.76850.71155.17555.1117.11.4875

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata processing
XDSFeb 5, 2021data reduction
Aimless0.7.7data scaling
STARANISO2.3.79data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZHI

5zhi


Resolution: 1.956→68.27 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.258 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.276 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.208
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1403 -RANDOM
Rwork0.2344 ---
obs0.2358 27639 60.3 %-
Displacement parametersBiso mean: 43.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.4716 Å20 Å20 Å2
2--0.4716 Å20 Å2
3----0.9431 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 1.956→68.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 0 226 3223
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083132HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.844275HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1050SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes537HARMONIC5
X-RAY DIFFRACTIONt_it3132HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion396SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2542SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion15.79
LS refinement shellResolution: 1.96→2.09 Å
RfactorNum. reflection% reflection
Rfree0.3128 35 -
Rwork0.3142 --
obs0.3141 553 6.99 %

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