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- PDB-7wm5: Crystal structure of apo TrmM from Mycoplasma capricolum -

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Basic information

Entry
Database: PDB / ID: 7wm5
TitleCrystal structure of apo TrmM from Mycoplasma capricolum
ComponentsMethyltransferase
KeywordsTRANSFERASE / t6A / 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
Biological speciesMycoplasma capricolum subsp. capricolum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase


Theoretical massNumber of molelcules
Total (without water)30,0491
Polymers30,0491
Non-polymers00
Water54030
1
A: Methyltransferase

A: Methyltransferase


Theoretical massNumber of molelcules
Total (without water)60,0972
Polymers60,0972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1990 Å2
ΔGint-12 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.710, 112.710, 110.178
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

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Components

#1: Protein Methyltransferase


Mass: 30048.598 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M Sodium chloride 10% w/v Polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 13888 / % possible obs: 93.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 40.09 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.039 / Rrim(I) all: 0.091 / Χ2: 0.805 / Net I/σ(I): 5.8 / Num. measured all: 71295
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.193.80.5676740.8980.3050.6490.46591.8
2.19-2.233.90.5397060.9090.2870.6150.46695.9
2.23-2.274.40.5797080.9240.2850.650.48696.5
2.27-2.3250.556940.940.250.6080.44795.7
2.32-2.375.20.4727040.9560.2120.5220.45296.4
2.37-2.425.30.4967120.9390.2190.5470.49495.2
2.42-2.485.30.4056890.9640.180.4470.46295.2
2.48-2.555.20.2937050.9750.1320.3240.49194.8
2.55-2.624.80.2696960.9670.130.3010.58994.1
2.62-2.715.10.2296980.9820.1060.2550.55394.2
2.71-2.815.10.1876900.980.0910.2110.65593.4
2.81-2.925.80.1546930.9810.070.1710.72193.6
2.92-3.055.70.1296880.9860.0590.1430.73193.4
3.05-3.215.70.1126940.9860.0540.1260.83893.2
3.21-3.415.60.0887040.9930.0410.0981.02193.4
3.41-3.675.60.0766850.9920.0360.0841.29892.3
3.67-4.045.50.0646880.9910.0310.0711.31792.3
4.04-4.6350.0566930.9920.0290.0641.43491.2
4.63-5.8250.0566800.9950.0270.0621.41989.1
5.82-305.90.0516870.9970.0220.0561.34886.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LPM

3lpm


Resolution: 2.15→26.51 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 738 5.32 %
Rwork0.2022 13130 -
obs0.2051 13868 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.49 Å2 / Biso mean: 49.2221 Å2 / Biso min: 31.28 Å2
Refinement stepCycle: final / Resolution: 2.15→26.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 0 30 1701
Biso mean---45.77 -
Num. residues----212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.310.32221420.2612627276995
2.31-2.540.30441570.24092654281195
2.54-2.910.31241370.22962636277394
2.91-3.670.3021580.20912620277893
3.67-26.510.20391440.17482593273789

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