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- PDB-8txa: Apo Structure of (N1G37) tRNA Methyltransferase from Mycobacteriu... -

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Basic information

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


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA modification / methylation / 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 marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 Å
AuthorsBalsamo, A. / Bruno, C. / Edele, C. / Fabian, T. / Jannotta, R. / Lee, R. / Schryver, D. / Warsaw, J. / Warsaw, L. / Stojanoff, V. ...Balsamo, A. / Bruno, C. / Edele, C. / Fabian, T. / Jannotta, R. / Lee, R. / Schryver, D. / Warsaw, J. / Warsaw, L. / Stojanoff, V. / Battaile, K. / 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) tRNA Methyltransferase from Mycobacterium marinum
Authors: Balsamo, A. / Bruno, C. / Edele, C. / Fabian, T. / Jannotta, R. / Lee, R. / Schryver, D. / Warsaw, J. / Warsaw, L. / Stojanoff, V. / Battaile, K. / Perez, A. / Bolen, R.
History
DepositionAug 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2024Provider: 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
C: tRNA (guanine-N(1)-)-methyltransferase
D: tRNA (guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)110,7174
Polymers110,7174
Non-polymers00
Water8,269459
1
A: tRNA (guanine-N(1)-)-methyltransferase
B: tRNA (guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)55,3592
Polymers55,3592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-15 kcal/mol
Surface area17640 Å2
MethodPISA
2
C: tRNA (guanine-N(1)-)-methyltransferase
D: tRNA (guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)55,3592
Polymers55,3592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-15 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.94, 60.797, 68.072
Angle α, β, γ (deg.)97.05, 111.99, 100.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
tRNA (guanine-N(1)-)-methyltransferase / TRNA (guanine9-N1)-methyltransferase


Mass: 27679.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Gene: trmD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z5YCU9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 459 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 ul of 0.2M MgCl2 0.1M Tris-HCl, pH 8.0; 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: CryoStream cold gas flow system covers a user selectable temperature range from 80 to 400 K
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2022
Details: 16-segment bimorph bending mirrors in a single stage vertical and a dual stage horizontal focusing. Compound refractive Be lens unit upstream of the final focusing mirrors
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.591→61.702 Å / Num. obs: 64981 / % possible obs: 85.8 % / Redundancy: 3.18 %
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: 0.996 / CC1/2 anomalous: 0.038 / Rmerge(I) obs: 0.0693 / Rpim(I) all: 0.0452 / Rrim(I) all: 0.0831 / AbsDiff over sigma anomalous: 0.752 / Baniso tensor eigenvalue 1: 0 Å2 / Baniso tensor eigenvalue 2: 10.9114 Å2 / Baniso tensor eigenvalue 3: 19.4259 Å2 / Baniso tensor eigenvector 1 ortho1: 0.7743 / Baniso tensor eigenvector 1 ortho2: 0.2227 / Baniso tensor eigenvector 1 ortho3: 0.5924 / Baniso tensor eigenvector 2 ortho1: 0.0243 / Baniso tensor eigenvector 2 ortho2: 0.9249 / Baniso tensor eigenvector 2 ortho3: -0.3794 / Baniso tensor eigenvector 3 ortho1: -0.6324 / Baniso tensor eigenvector 3 ortho2: 0.3081 / Baniso tensor eigenvector 3 ortho3: 0.7107 / Aniso diffraction limit 1: 1.59 Å / Aniso diffraction limit 2: 1.826 Å / Aniso diffraction limit 3: 2.005 Å / Aniso diffraction limit axis 1 ortho1: 0.72542 / Aniso diffraction limit axis 1 ortho2: 0.10791 / Aniso diffraction limit axis 1 ortho3: 0.67981 / Aniso diffraction limit axis 2 ortho1: 0.10064 / Aniso diffraction limit axis 2 ortho2: 0.96037 / Aniso diffraction limit axis 2 ortho3: -0.25983 / Aniso diffraction limit axis 3 ortho1: -0.68093 / Aniso diffraction limit axis 3 ortho2: 0.25699 / Aniso diffraction limit axis 3 ortho3: 0.68582 / Net I/σ(I): 8.67 / Num. measured all: 206326 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 79.1 / % possible ellipsoidal: 85.8 / % possible ellipsoidal anomalous: 79.1 / % possible spherical: 59.5 / % possible spherical anomalous: 54.8 / Redundancy anomalous: 1.67 / 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
5.125-61.7023.20.034921.981038910389324932490.9920.0830.02310.04210.7019399.59399.5931.6799.5
4.062-5.1213.240.038321.741052510525324932490.997-0.0310.02490.04580.7119499.29499.2941.6799.2
3.493-4.0623.320.043820.221078110781324932490.996-0.0080.02820.05230.76381.885.981.885.981.81.7185.9
3.16-3.4923.210.054616.551041410414324932490.9950.0810.03530.06530.76884.890.484.890.484.81.6790.4
2.944-3.163.190.067413.951035310353324932490.993-0.0560.04370.08070.78391.898.591.898.591.81.6698.5
2.777-2.9443.040.081111.5198869886324932490.98800.05410.09790.79489.898.489.898.489.81.6198.4
2.625-2.7773.150.10199.741023310233324932490.9850.060.06670.12230.81378.185.578.185.578.11.6685.5
2.514-2.6253.260.1119.121060310603324932490.9860.0720.07130.13230.78892.698.192.698.192.61.6998.1
2.421-2.5143.320.13217.91079410794324932490.9820.0310.0840.1570.78593.397.993.397.993.31.7197.9
2.34-2.4213.330.1516.921083210832325032500.980.0630.0960.17940.77793.297.893.297.893.21.7197.8
2.269-2.343.350.18575.961086810868324932490.9670.040.11770.22040.77893.497.693.497.693.41.7297.6
2.194-2.2693.020.20394.9898289828324932490.9560.0470.13490.24550.77372.981.772.981.772.91.6281.7
2.139-2.1943.160.24274.441026110261324932490.9460.0940.15930.29150.76891.197.591.197.591.11.6497.5
2.088-2.1393.210.29113.821042510425324932490.9240.0330.18870.34810.73990.79790.79790.71.6797
2.032-2.0882.890.3427393879387324932490.8820.010.2360.41820.73168.878.768.878.768.81.5678.7
1.987-2.0323.170.37482.961029510295324932490.8760.0180.24460.4490.71584.490.384.489.783.81.6590.3
1.931-1.9873.040.43472.4698749874324932490.81-0.0430.28770.52310.70364.271.464.264.357.91.6271.4
1.861-1.9312.930.44782.2595219521324932490.8060.0320.29980.54090.71351.760.251.745.4391.660.2
1.783-1.8613.330.53862.211082110821324932490.7980.0290.34340.64040.72964.768.464.735.133.21.7268.4
1.591-1.7833.150.65331.721023610236324932490.712-0.0070.42310.78110.70552.163.852.110.28.31.7463.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata processing
PHENIXphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.591→22.98 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.143 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.143 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 3210 -RANDOM
Rwork0.1876 ---
obs0.1894 64946 59.5 %-
Displacement parametersBiso mean: 27.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.2422 Å2-0.524 Å2-2.7629 Å2
2--0.5809 Å2-0.1307 Å2
3----0.3387 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.591→22.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5955 0 0 459 6414
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016088HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.948297HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2013SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1022HARMONIC5
X-RAY DIFFRACTIONt_it6088HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion796SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5544SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion15.38
LS refinement shellResolution: 1.591→1.71 Å
RfactorNum. reflection% reflection
Rfree0.2797 78 -
Rwork0.2372 --
obs--6.03 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8566-0.04241.2796-0.09330.09191.1132-0.15190.003-0.10230.003-0.00350.0103-0.10230.01030.1554-0.0021-0.0056-0.0733-0.063-0.00460.0179-4.3929-29.315130.5656
20.49510.12890.43830.03690.08650.56390.00790.0166-0.02360.0166-0.0162-0.0369-0.0236-0.03690.0083-0.0011-0.0087-0.023-0.02030.0124-0.0041-6.5996-39.025221.9994
30.46690.10730.79390.37660.25461.061-0.0504-0.00580.026-0.0058-0.0321-0.02560.026-0.02560.0824-0.0398-0.00090.00660.0219-0.0148-0.02940.3753-3.86013.4863
40.79970.21881.06730.3488-0.02311.3688-0.01030.0210.03650.0210.00550.03810.03650.03810.0048-0.03190.0046-0.017-0.02410.0076-0.014813.3064-1.694.5918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 226
2X-RAY DIFFRACTION2{ B|* }B-1 - 226
3X-RAY DIFFRACTION3{ C|* }C1 - 227
4X-RAY DIFFRACTION4{ D|* }D0 - 223

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