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- PDB-6w15: Crystal structure of tRNA (guanine-N(1)-)-methyltransferase with ... -

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Basic information

Entry
Database: PDB / ID: 6w15
TitleCrystal structure of tRNA (guanine-N(1)-)-methyltransferase with bound SAH from Mycobacterium smegmatis
ComponentstRNA (guanine-N(1)-)-methyltransferaseTRNA (guanine9-N1)-methyltransferase
KeywordsTRANSFERASE / SSGCID / tRNA (guanine-N(1)-)-methyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine-N(1)-)-methyltransferase / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of tRNA (guanine-N(1)-)-methyltransferase with bound SAH from Mycobacterium smegmatis
Authors: Dranow, D.M. / Bolejack, M.J. / Abendroth, J.A. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4422
Polymers26,0571
Non-polymers3841
Water1,08160
1
A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules

A: tRNA (guanine-N(1)-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8834
Polymers52,1152
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6700 Å2
ΔGint-8 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 59.100, 114.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 26057.330 Da / Num. of mol.: 1 / Fragment: MysmA.00937.a.AE1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: trmD, MSMEI_2377 / Plasmid: MysmA.00937.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I7FBD0, UniProt: A0QV40*PLUS, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.92 Å3/Da / Density % sol: 35.92 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MysmA.00937.a.AE1.PW38670 at 19.05 mg/ml, incubated with 5 mM SAH, mixed 1:1 with MCSG1(a10): 28% (v/v) PPG P400, 0.1 M HEPES:NaOH, pH = 7.5, 0.2 M CaCl2. Tray: 311562a10. Puck: dcp5-10.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14157 / % possible obs: 98.4 % / Redundancy: 24.126 % / Biso Wilson estimate: 44.465 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.038 / Χ2: 0.982 / Net I/σ(I): 55.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.0516.1590.6214.7610430.9870.64299.9
2.05-2.1117.8110.5026.2710050.9750.51699.8
2.11-2.1719.5510.4048.579660.9860.41599.4
2.17-2.2420.5420.30611.829410.9970.31498.9
2.24-2.3121.8250.24814.759100.9960.25497.4
2.31-2.3923.780.18220.158950.9980.18697.8
2.39-2.4826.3750.15325.398370.9990.15697
2.48-2.5827.8740.13229.578120.9990.13496.4
2.58-2.727.8510.10536.878110.9990.10798.3
2.7-2.8327.8230.08343.937410.9990.08497.4
2.83-2.9827.8810.05958.6372510.0697.4
2.98-3.1627.9010.04476.5669510.04599
3.16-3.3827.7020.03690.3365210.03797.6
3.38-3.6527.4810.028116.8261710.02899
3.65-427.2530.023139.7957010.02498.6
4-4.4726.7140.02150.9452110.0298.7
4.47-5.1626.6030.018159.9347310.01899.6
5.16-6.3225.8920.02156.6540810.0299.5
6.32-8.9424.6340.018159.3432810.019100
8.94-5020.4110.017161.1920710.01898.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZHI

5zhi


Resolution: 2→41.79 Å / SU ML: 0.2308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4062
RfactorNum. reflection% reflection
Rfree0.2629 1373 9.71 %
Rwork0.203 --
obs0.2087 14147 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.38 Å2
Refinement stepCycle: LAST / Resolution: 2→41.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 26 60 1643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621620
X-RAY DIFFRACTIONf_angle_d0.80532211
X-RAY DIFFRACTIONf_chiral_restr0.0523249
X-RAY DIFFRACTIONf_plane_restr0.0045301
X-RAY DIFFRACTIONf_dihedral_angle_d18.0736603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.32331490.26751240X-RAY DIFFRACTION99.71
2.07-2.150.29751500.25481254X-RAY DIFFRACTION99.57
2.15-2.250.30971390.23521243X-RAY DIFFRACTION98.43
2.25-2.370.34391300.24411251X-RAY DIFFRACTION97.6
2.37-2.520.26881310.23651229X-RAY DIFFRACTION97.35
2.52-2.710.32661350.24861253X-RAY DIFFRACTION97.27
2.71-2.990.32781240.25171274X-RAY DIFFRACTION97.22
2.99-3.420.30141230.22271285X-RAY DIFFRACTION98.32
3.42-4.30.22771430.16481325X-RAY DIFFRACTION98.92
4.31-41.790.21351490.17261420X-RAY DIFFRACTION99.3
Refinement TLS params.

Method: refined / 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)
18.7970822605-1.94382466497-6.410610527474.09535287441.916498755114.723898799630.108012084704-0.04168319323460.362934394379-0.1972539736380.2373898266170.00572815115351-0.9957982729210.503635099226-0.3643323424210.415629957967-0.0953516069469-0.06908644943990.392630008997-0.08536160509310.34369613999913.48793252238.754296289849.383108724
27.90214839523-5.21888111754-3.388568213975.51596686192.261203673122.6341161578-0.338876410309-0.6756739838670.3467118096350.2460053087520.529221457494-0.780899748023-0.1177369382380.761632179473-0.2494403555280.321966667967-0.0664891182019-0.06525894114830.494160252215-0.1635876020420.51719679129425.04535900892.006092635399.14185797969
33.2600401372-1.85697835627-1.438585066544.432477565032.272751149274.41131604252-0.193706457501-0.5378550413570.1217182118650.5442391857310.454812437598-0.4798718667770.5215439961480.662179557842-0.3633780667340.3872145614570.0473270685581-0.09249952816610.300950337496-0.05027565768780.36441789035819.3292327083-7.468420108559.8740182246
42.78017912351-1.22188950327-0.2477215832624.175362919791.805912250383.52441692049-0.146039938229-0.29250727368-0.06400080948870.4406847154330.286173304663-0.007014865018550.4533304849650.0736362100697-0.1498647561020.304028921371-0.0763512287232-0.001636487391610.2465023478630.009516096235380.2392811962147.27603793381-2.40490345559.62825071995
55.62613641627-0.313116478074.359345279970.0586022604285-0.1924506811773.52559066885-0.19751782953-0.0315688010315-0.1011723569350.3053491232910.3470051451520.101723533285-0.364585572373-0.266591871265-0.05828911804810.334534906596-0.07615723629630.06063669730420.425485380438-0.01686852190280.468670510509-13.35749810248.672155319753.84956420237
65.444852059463.01244765019-0.7809845481162.35500609961-1.351437299231.691755544720.8506839934471.025516121091.19178848723-0.557008340564-0.487085542350.497460872297-0.880290981343-0.14832317727-0.3856559424730.494753703170.2778264086890.05232665220840.8039173600520.1023879111550.521361467088-21.245147847421.6459933501-9.21367745219
77.97923892622-5.55605128823-0.838623766014.497241346650.8518441997541.13442564928-0.05265774612270.712791652027-0.9807288334590.14682003664-0.3951420816090.8522136284790.377700625006-0.6467913854910.4213035020560.469618295602-0.224775055051-0.004098442980630.775521406163-0.1891511164750.539474927754-20.98984844814.75719251503-2.56958788545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 180 )
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 200 )
7X-RAY DIFFRACTION7chain 'A' and (resid 201 through 225 )

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