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- PDB-7rf0: MYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN COMPLEX WITH S-... -

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Basic information

Entry
Database: PDB / ID: 7rf0
TitleMYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE AND MAGNESIUM
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / MYCOBACTERIUM ABSCESSUS
Function / homology
Function and homology information


tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA N1-guanine methylation / metal ion binding / cytosol
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 TrmD / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsPrucha, G.R. / Ismail, M. / Suske, A. / Das, B. / Oz, M. / Perez, A. / Bolen, R. / Jayaraman, S. / Stojanoff, V. / Halloran, J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
Department of Energy (DOE, United States)KP1605010 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
Other private United States
CitationJournal: To Be Published
Title: Crystal structure of divalent Mg+2 dependent Mycobacterium abscessus tRNA (m1 G37) Methyltransferase (TrmD)
Authors: Prucha, G.R. / Ismail, M. / Suske, A. / Perez, A. / Bolen, R. / Jayaraman, S. / Stojanoff, V. / Halloran, J.
History
DepositionJul 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7978
Polymers50,9312
Non-polymers8666
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-54 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.398, 78.835, 86.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25465.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria)
Gene: trmD, SAMEA2161603_03547, SAMEA2275821_02238, SAMEA2275847_06627
Production host: Escherichia coli (E. coli)
References: UniProt: A0A1M9INC4, tRNA (guanine37-N1)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Drops were 2ul of protein 24 mg/ml and 2ul buffer (0.1M sodium cacodylate and 2M ammonium nitrate pH 6.5); co-crystallized with SAH in a 1:1 ratio at a final concentration of 5mM SAH in the ...Details: Drops were 2ul of protein 24 mg/ml and 2ul buffer (0.1M sodium cacodylate and 2M ammonium nitrate pH 6.5); co-crystallized with SAH in a 1:1 ratio at a final concentration of 5mM SAH in the drops; and 4ul MgSO4 at 10mM were added to the drops before cryo-cooling

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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: 0.9802 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 2, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9802 Å / Relative weight: 1
ReflectionResolution: 1.56→28.24 Å / Num. obs: 68820 / % possible obs: 99.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.77 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.8
Reflection shellResolution: 1.56→1.6 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4995 / CC1/2: 0.781

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
ADDREFdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVR

6nvr


Resolution: 1.59→28.22 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 3600 5.23 %RANDOM
Rwork0.1802 ---
obs0.1819 68820 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→28.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 56 314 3631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063442
X-RAY DIFFRACTIONf_angle_d0.984714
X-RAY DIFFRACTIONf_dihedral_angle_d15.586512
X-RAY DIFFRACTIONf_chiral_restr0.063538
X-RAY DIFFRACTIONf_plane_restr0.01603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.29931580.27262462X-RAY DIFFRACTION99
1.61-1.630.3181240.26132453X-RAY DIFFRACTION99
1.63-1.660.27441440.24922475X-RAY DIFFRACTION100
1.66-1.680.22551540.23142422X-RAY DIFFRACTION99
1.68-1.710.24171570.21762451X-RAY DIFFRACTION99
1.71-1.740.26271590.2232441X-RAY DIFFRACTION99
1.74-1.760.33231330.26072479X-RAY DIFFRACTION100
1.77-1.80.30961560.24912482X-RAY DIFFRACTION100
1.8-1.830.26281490.21712473X-RAY DIFFRACTION100
1.83-1.870.22741370.19932491X-RAY DIFFRACTION100
1.87-1.910.24121440.18592471X-RAY DIFFRACTION99
1.91-1.950.21861150.18332519X-RAY DIFFRACTION100
1.95-20.19911170.17922513X-RAY DIFFRACTION100
2-2.060.23281120.18792510X-RAY DIFFRACTION100
2.06-2.120.20191330.19182544X-RAY DIFFRACTION100
2.12-2.190.2051440.17862468X-RAY DIFFRACTION100
2.19-2.260.20351590.17412483X-RAY DIFFRACTION100
2.26-2.350.19271210.1742520X-RAY DIFFRACTION100
2.35-2.460.21371250.17472546X-RAY DIFFRACTION100
2.46-2.590.20851080.17682542X-RAY DIFFRACTION100
2.59-2.750.25671070.19532559X-RAY DIFFRACTION100
2.75-2.970.21571480.19092537X-RAY DIFFRACTION100
2.97-3.260.231210.1782569X-RAY DIFFRACTION100
3.26-3.740.19121110.15932591X-RAY DIFFRACTION99
3.74-4.70.17471680.14762563X-RAY DIFFRACTION100
4.7-28.220.20721960.17652656X-RAY DIFFRACTION99

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