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- PDB-8q56: Phage defense complex -

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Basic information

Entry
Database: PDB / ID: 8q56
TitlePglX methyltransferase of Salmonella BREX phage defence system (aka BrxX) bound to inhibitor Ocr
Components
  • Protein Ocr
  • site-specific DNA-methyltransferase (adenine-specific)
KeywordsDNA BINDING PROTEIN / Methyltransferase / Phage defense / DNA binding
Function / homology
Function and homology information


symbiont-mediated evasion of host restriction-modification system / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA modification / methylation / nucleic acid binding / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response
Similarity search - Function
: / B-form DNA mimic Ocr / DNA mimic ocr / Protein Ocr / 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) / Protein Ocr
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. D23580 (bacteria)
Escherichia phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWent, S.C. / Blower, T.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)EP/S022791/1 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
DepositionAug 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)155,7253
Polymers155,3262
Non-polymers3981
Water362
1
A: site-specific DNA-methyltransferase (adenine-specific)
B: Protein Ocr
hetero molecules

A: site-specific DNA-methyltransferase (adenine-specific)
B: Protein Ocr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,4506
Polymers310,6534
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)238.458, 60.786, 146.637
Angle α, β, γ (deg.)90.000, 114.890, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 141507.359 Da / Num. of mol.: 1
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: Protein Protein Ocr


Mass: 13819.015 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T7 (virus) / Gene: 0.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03775
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.1 M NaCl, 0.1 M KCl, 14% PEG 4000, 6% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→59.61 Å / Num. obs: 24038 / % possible obs: 97.84 % / Redundancy: 1.9 % / Biso Wilson estimate: 127.38 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Net I/σ(I): 3.8
Reflection shellResolution: 3.5→3.625 Å / Rmerge(I) obs: 0.756 / Num. unique obs: 2462 / CC1/2: 0.378

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→59.61 Å / SU ML: 0.7671 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.5052
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2917 1922 8 %
Rwork0.2462 22118 -
obs0.2518 24038 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 138.5 Å2
Refinement stepCycle: LAST / Resolution: 3.5→59.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10747 0 27 2 10776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003311011
X-RAY DIFFRACTIONf_angle_d0.751314904
X-RAY DIFFRACTIONf_chiral_restr0.04631610
X-RAY DIFFRACTIONf_plane_restr0.00591934
X-RAY DIFFRACTIONf_dihedral_angle_d13.55834103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.44421060.41261287X-RAY DIFFRACTION79.6
3.59-3.680.40021150.39791455X-RAY DIFFRACTION92.24
3.68-3.790.37271460.35751607X-RAY DIFFRACTION99.66
3.79-3.920.35851230.34331567X-RAY DIFFRACTION99.82
3.92-4.060.33291530.3161626X-RAY DIFFRACTION99.83
4.06-4.220.32841280.30191582X-RAY DIFFRACTION100
4.22-4.410.3121480.27281619X-RAY DIFFRACTION99.89
4.41-4.640.30471340.26591591X-RAY DIFFRACTION99.94
4.64-4.930.28321510.25521598X-RAY DIFFRACTION99.94
4.93-5.310.36941240.26721627X-RAY DIFFRACTION100
5.31-5.850.35631340.25081626X-RAY DIFFRACTION99.94
5.85-6.690.31181480.25171622X-RAY DIFFRACTION99.89
6.69-8.430.24291590.20541617X-RAY DIFFRACTION99.94
8.43-59.610.22591530.16461694X-RAY DIFFRACTION99.3

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