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- PDB-7wm6: Crystal structure of SAH-bound TrmM from Mycoplasma capricolum -

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Basic information

Entry
Database: PDB / ID: 7wm6
TitleCrystal structure of SAH-bound TrmM from Mycoplasma capricolum
ComponentsMethyltransferase
KeywordsTRANSFERASE / tRNA / m6A / methyltransferase
Function / homology
Function and homology information


N-methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / methylation / nucleic acid binding / cytoplasm
Similarity search - Function
: / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesMycoplasma capricolum subsp. capricolum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsJeong, H. / Kim, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Protein Sci. / Year: 2022
Title: Structural and functional characterization of TrmM in m 6 A modification of bacterial tRNA.
Authors: Jeong, H. / Lee, Y. / Kim, J.
History
DepositionJan 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
C: Methyltransferase
D: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4749
Polymers115,1294
Non-polymers1,3455
Water55831
1
A: Methyltransferase
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0454
Polymers57,5652
Non-polymers4802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-21 kcal/mol
Surface area17990 Å2
MethodPISA
2
C: Methyltransferase
D: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4295
Polymers57,5652
Non-polymers8653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-22 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.390, 75.890, 95.540
Angle α, β, γ (deg.)90.000, 95.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methyltransferase


Mass: 28782.285 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma capricolum subsp. capricolum (bacteria)
Gene: MCGM508_01850
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0C2W699
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 0.2 M Ammonium sulfate 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.54→47.64 Å / Num. obs: 34219 / % possible obs: 97.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 46 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.093 / Rrim(I) all: 0.235 / Net I/σ(I): 6.9 / Num. measured all: 210998 / Scaling rejects: 1625
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.54-2.6562.3852484141610.4131.0462.6121.496.9
8.8-47.645.80.06549908530.9940.0290.07219.295.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LPM

3lpm


Resolution: 2.54→47.64 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2664 1667 4.88 %
Rwork0.2093 32458 -
obs0.2121 34125 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.6 Å2 / Biso mean: 54.6667 Å2 / Biso min: 21.46 Å2
Refinement stepCycle: final / Resolution: 2.54→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6929 0 88 31 7048
Biso mean--56.58 39.71 -
Num. residues----891
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.54-2.610.42981330.34032634276795
2.61-2.70.38291420.32172685282798
2.7-2.80.37351550.28722708286398
2.8-2.910.33111510.26542689284098
2.91-3.040.34731550.25232664281996
3.04-3.20.2941000.25042678277895
3.2-3.40.28561300.2082748287899
3.4-3.660.25881530.19462710286398
3.66-4.030.2316860.19062752283897
4.03-4.610.19141550.16322692284796
4.61-5.810.25821480.17972760290898
5.81-47.640.22781590.18882738289796

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