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- PDB-8c45: PglX methyltransferase from the Salmonella BREX phage defence sys... -

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Basic information

Entry
Database: PDB / ID: 8c45
TitlePglX methyltransferase from the Salmonella BREX phage defence system (aka BrxX)
Componentssite-specific DNA-methyltransferase (adenine-specific)
KeywordsDNA BINDING PROTEIN / Phage defence
Function / homology
Function and homology information


DNA modification / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / methylation / nucleic acid binding
Similarity search - Function
: / Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification methylase / : / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. D23580 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBlower, T.R. / Went, S.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence.
Authors: Went, S.C. / Picton, D.M. / Morgan, R.D. / Nelson, A. / Brady, A. / Mariano, G. / Dryden, D.T.F. / Smith, D.L. / Wenner, N. / Hinton, J.C.D. / Blower, T.R.
History
DepositionJan 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: site-specific DNA-methyltransferase (adenine-specific)
B: site-specific DNA-methyltransferase (adenine-specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,8124
Polymers283,0152
Non-polymers7972
Water00
1
A: site-specific DNA-methyltransferase (adenine-specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,9062
Polymers141,5071
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: site-specific DNA-methyltransferase (adenine-specific)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,9062
Polymers141,5071
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.539, 138.539, 407.956
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein site-specific DNA-methyltransferase (adenine-specific)


Mass: 141507.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. D23580 (bacteria)
Gene: STMMW_44401 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A6C7IK61, site-specific DNA-methyltransferase (adenine-specific)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
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: 3.46 Å3/Da / Density % sol: 64.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 15% PEG 3000 MME 0.1 M Tris pH 7.5 0.1 M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→70.65 Å / Num. obs: 55797 / % possible obs: 99.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 159.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.067 / Net I/σ(I): 8
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 1.9 % / Rmerge(I) obs: 1.515 / Num. unique obs: 4461 / CC1/2: 0.214 / Rrim(I) all: 2.142 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
xia2.multiplexdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→61.72 Å / SU ML: 0.5724 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.6045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2805 4289 5.13 %
Rwork0.2653 79310 -
obs0.2661 55797 87.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 168.05 Å2
Refinement stepCycle: LAST / Resolution: 3.5→61.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19794 0 54 0 19848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004620288
X-RAY DIFFRACTIONf_angle_d0.911527451
X-RAY DIFFRACTIONf_chiral_restr0.05092966
X-RAY DIFFRACTIONf_plane_restr0.00613551
X-RAY DIFFRACTIONf_dihedral_angle_d24.69087564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.540.4427250.4413360X-RAY DIFFRACTION12.23
3.54-3.580.4882200.4513342X-RAY DIFFRACTION11.46
3.58-3.630.4767200.4402424X-RAY DIFFRACTION14.1
3.63-3.670.4402890.4151936X-RAY DIFFRACTION64.02
3.67-3.720.43851290.39681785X-RAY DIFFRACTION60.65
3.72-3.770.38351200.37812036X-RAY DIFFRACTION66.38
3.77-3.820.33311320.37763038X-RAY DIFFRACTION99.69
3.82-3.880.37631410.37463031X-RAY DIFFRACTION100
3.88-3.940.35611520.34513037X-RAY DIFFRACTION100
3.94-4.010.31681620.3383002X-RAY DIFFRACTION100
4.01-4.080.34361550.31943101X-RAY DIFFRACTION100
4.08-4.150.32221500.31862953X-RAY DIFFRACTION100
4.15-4.230.29411870.33046X-RAY DIFFRACTION99.94
4.23-4.320.32641490.31133045X-RAY DIFFRACTION100
4.32-4.410.31441860.30122957X-RAY DIFFRACTION100
4.41-4.510.31941480.29833035X-RAY DIFFRACTION100
4.51-4.620.29871670.2983075X-RAY DIFFRACTION100
4.62-4.750.31650.2842994X-RAY DIFFRACTION100
4.75-4.890.36892000.2882973X-RAY DIFFRACTION100
4.89-5.050.27581540.28273045X-RAY DIFFRACTION100
5.05-5.230.32081660.28453008X-RAY DIFFRACTION100
5.23-5.440.33851740.28633029X-RAY DIFFRACTION100
5.44-5.680.31511710.29012994X-RAY DIFFRACTION100
5.68-5.980.32041400.28633067X-RAY DIFFRACTION100
5.98-6.360.33861740.28113003X-RAY DIFFRACTION100
6.36-6.850.30031670.27493037X-RAY DIFFRACTION100
6.85-7.540.28411710.25933029X-RAY DIFFRACTION100
7.54-8.620.22891620.2293021X-RAY DIFFRACTION100
8.62-10.860.17511780.17512991X-RAY DIFFRACTION99.78
10.86-61.720.20831350.21172916X-RAY DIFFRACTION95.55

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