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- PDB-7eew: Crystal structure of the intact MTase from Vibrio vulnificus YJ01... -

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Basic information

Entry
Database: PDB / ID: 7eew
TitleCrystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH)
Components
  • Overcome classical restriction gp0.3
  • Type I restriction-modification system methyltransferase subunit
KeywordsTRANSFERASE / Type I restriction-modification system / Methyltransferase / Ocr
Function / homology
Function and homology information


symbiont-mediated evasion of host restriction-modification system / N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / DNA restriction-modification system / methylation / symbiont-mediated suppression of host innate immune response / : / DNA binding
Similarity search - Function
B-form DNA mimic Ocr / DNA mimic ocr / Protein Ocr / : / Type I restriction modification DNA specificity domain / Type I restriction modification DNA specificity domain superfamily / Type I restriction modification DNA specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Protein Ocr / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
Escherichia phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.896 Å
AuthorsSeo, P.W. / Park, S.Y. / Kim, J.S.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2018M3D3A1A01055735 Korea, Republic Of
Rural Development AdministrationNRF-2019R1F1A1063023 Korea, Republic Of
Rural Development AdministrationNRF-2020R1F1A1054849 Korea, Republic Of
Rural Development AdministrationNRF-2018R1A5A2024181 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structural features of a minimal intact methyltransferase of a type I restriction-modification system.
Authors: Seo, P.W. / Hofmann, A. / Kim, J.H. / Hwangbo, S.A. / Kim, J.H. / Kim, J.W. / Huynh, T.Y.L. / Choy, H.E. / Kim, S.J. / Lee, J. / Lee, J.O. / Jin, K.S. / Park, S.Y. / Kim, J.S.
History
DepositionMar 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Type I restriction-modification system methyltransferase subunit
B: Overcome classical restriction gp0.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0743
Polymers85,6902
Non-polymers3841
Water1,08160
1
A: Type I restriction-modification system methyltransferase subunit
B: Overcome classical restriction gp0.3
hetero molecules

A: Type I restriction-modification system methyltransferase subunit
B: Overcome classical restriction gp0.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,1496
Polymers171,3804
Non-polymers7692
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area9800 Å2
ΔGint-65 kcal/mol
Surface area70310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.280, 133.280, 236.808
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-817-

HOH

21A-853-

HOH

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Components

#1: Protein Type I restriction-modification system methyltransferase subunit


Mass: 71870.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (strain YJ016) (bacteria)
Strain: YJ016 / Gene: VV2202 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q7MJG0
#2: Protein Overcome classical restriction gp0.3 / Gene product 0.3 / Gp0.3 / 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 K-12 (bacteria) / References: UniProt: P03775
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.54 Å3/Da / Density % sol: 65.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% (w/v) polyethylene glycol 6000, 0.1 M sodium chloride, 0.1 M HEPES pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.896→20 Å / Num. obs: 27924 / % possible obs: 98.6 % / Redundancy: 13.8 % / Biso Wilson estimate: 59.53 Å2 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.05 / Rrim(I) all: 0.195 / Net I/σ(I): 13.6
Reflection shellResolution: 2.896→2.95 Å / Rmerge(I) obs: 0.758 / Num. unique obs: 1327 / Rpim(I) all: 0.343 / Rrim(I) all: 0.837

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.896→14.956 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 2.3 / Phase error: 33.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2932 1312 4.96 %
Rwork0.2715 25120 -
obs0.2726 26432 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.21 Å2 / Biso mean: 63.6735 Å2 / Biso min: 11.75 Å2
Refinement stepCycle: final / Resolution: 2.896→14.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5743 0 26 60 5829
Biso mean--52.28 39.82 -
Num. residues----720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025870
X-RAY DIFFRACTIONf_angle_d0.5057934
X-RAY DIFFRACTIONf_chiral_restr0.038903
X-RAY DIFFRACTIONf_plane_restr0.0041013
X-RAY DIFFRACTIONf_dihedral_angle_d16.6613532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.896-3.01060.40441260.4044239983
3.0106-3.14650.40751320.3699262190
3.1465-3.31060.35161390.3264270392
3.3106-3.51550.32031490.3056277995
3.5155-3.78290.32521470.2823280095
3.7829-4.15620.30031480.273284596
4.1562-4.74070.26891480.2424290697
4.7407-5.91090.2941580.2703295298
5.9109-14.95570.22311650.2099311598

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