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

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Basic information

Entry
Database: PDB / ID: 7rez
TitleMYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE
ComponentstRNA (guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / Methyltransferase / Mycobacterium Abscessus / S-Adenosyl-L-homocysteine
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: 1.64 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)DE-SC0012704 United States
Department of Energy (DOE, United States)KP1605010 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

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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)51,7004
Polymers50,9312
Non-polymers7692
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-17 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.242, 79.094, 86.631
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein at 24mg/ml was incubated with 10mM SAH in DMSO in a 1 to 1 ratio; Buffer 2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5. Drops were formed 1 to 1 ratio and crystals cryo ...Details: Protein at 24mg/ml was incubated with 10mM SAH in DMSO in a 1 to 1 ratio; Buffer 2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5. Drops were formed 1 to 1 ratio and crystals cryo protected by adding 1 microliter of 50 percent Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.64→29.22 Å / Num. obs: 63130 / % possible obs: 99.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 25.4 Å2 / CC1/2: 1 / Net I/σ(I): 0.699
Reflection shellResolution: 1.64→1.681 Å / Num. unique obs: 4406 / CC1/2: 0.87 / % possible all: 95.5

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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: 1.64→29.21 Å / SU ML: 0.1913 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1937
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 3153 5 %RANDOM
Rwork0.1865 59894 --
obs0.188 63047 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.26 Å2
Refinement stepCycle: LAST / Resolution: 1.64→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 52 389 3734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643492
X-RAY DIFFRACTIONf_angle_d0.97444790
X-RAY DIFFRACTIONf_chiral_restr0.0625549
X-RAY DIFFRACTIONf_plane_restr0.0114611
X-RAY DIFFRACTIONf_dihedral_angle_d15.832527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.3131170.26632359X-RAY DIFFRACTION92.15
1.66-1.690.26971280.22912607X-RAY DIFFRACTION100
1.69-1.720.24291310.21532582X-RAY DIFFRACTION100
1.72-1.750.22381380.20272577X-RAY DIFFRACTION100
1.75-1.780.23521550.19342569X-RAY DIFFRACTION100
1.78-1.810.24931240.19152604X-RAY DIFFRACTION100
1.81-1.850.23051040.19142612X-RAY DIFFRACTION100
1.85-1.890.24311460.19052572X-RAY DIFFRACTION100
1.89-1.930.22541490.2022581X-RAY DIFFRACTION99.74
1.93-1.980.24911320.19052592X-RAY DIFFRACTION99.96
1.98-2.040.21271450.19842577X-RAY DIFFRACTION100
2.04-2.10.20881280.19622593X-RAY DIFFRACTION100
2.1-2.160.21061330.19142603X-RAY DIFFRACTION100
2.16-2.240.24211300.18672622X-RAY DIFFRACTION99.93
2.24-2.330.24521250.19082617X-RAY DIFFRACTION99.93
2.33-2.440.21081310.20042622X-RAY DIFFRACTION99.96
2.44-2.560.23141410.19532604X-RAY DIFFRACTION99.96
2.56-2.720.24841510.21352613X-RAY DIFFRACTION99.96
2.72-2.930.29481470.22532613X-RAY DIFFRACTION100
2.93-3.230.23231570.20392626X-RAY DIFFRACTION100
3.23-3.70.19211570.1732639X-RAY DIFFRACTION100
3.7-4.650.17531490.14742689X-RAY DIFFRACTION99.96
4.65-29.210.17711350.17162821X-RAY DIFFRACTION100

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