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- PDB-7rey: MYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN APO FORM -

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Basic information

Entry
Database: PDB / ID: 7rey
TitleMYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN APO FORM
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 modification / methylation / metal ion binding / 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 speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 Mg2+ 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 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)50,9774
Polymers50,9312
Non-polymers462
Water8,611478
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-42 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.785, 79.375, 86.604
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2ul protein at concentration 24mg/ml, and 2ul buffer (0.1 M sodium cacodylate, 2 M ammonium sulfate pH 6.5), 1uL 50% Glycerol

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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: 0.92 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: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.87→29.26 Å / Num. obs: 42678 / % possible obs: 99 % / Observed criterion σ(F): 0.054 / Observed criterion σ(I): 0.656 / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2711 / CC1/2: 0.612 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NVR

6nvr


Resolution: 1.87→29.26 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.396 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22625 2116 5 %RANDOM
Rwork0.17418 ---
obs0.17688 40498 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.328 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.87→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 2 478 3780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133415
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173227
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.6424667
X-RAY DIFFRACTIONr_angle_other_deg1.3681.5777423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36520.69174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02615525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5591531
X-RAY DIFFRACTIONr_chiral_restr0.0790.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02751
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0863.6151740
X-RAY DIFFRACTIONr_mcbond_other3.0743.6131739
X-RAY DIFFRACTIONr_mcangle_it4.375.3912168
X-RAY DIFFRACTIONr_mcangle_other4.375.3942169
X-RAY DIFFRACTIONr_scbond_it4.1524.0041675
X-RAY DIFFRACTIONr_scbond_other4.1514.0071676
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2655.8332500
X-RAY DIFFRACTIONr_long_range_B_refined16.25548.6454213
X-RAY DIFFRACTIONr_long_range_B_other15.84447.6014070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.913 Å
RfactorNum. reflection% reflection
Rfree0.387 141 -
Rwork0.372 2559 -
obs--86.68 %

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