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- PDB-7p9k: BrxU, GmrSD-family Type IV restriction enzyme -

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Basic information

Entry
Database: PDB / ID: 7p9k
TitleBrxU, GmrSD-family Type IV restriction enzyme
ComponentsDUF262 domain-containing protein
KeywordsDNA BINDING PROTEIN / Restriction endonuclease / Phage defence protein
Function / homologyDomain of unknown function DUF262 / Protein of unknown function DUF262 / DUF262 domain-containing protein
Function and homology information
Biological speciesEscherichia fergusonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsPicton, D.M. / Luyten, Y. / Morgan, R.D. / Nelson, A. / Smith, D.L. / Dryden, D.T.F. / Hinton, J.C.D. / Blower, T.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011186/1 United Kingdom
Other privateLister Insitute of Preventative Medicine Prize Fellowship United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses.
Authors: Picton, D.M. / Luyten, Y.A. / Morgan, R.D. / Nelson, A. / Smith, D.L. / Dryden, D.T.F. / Hinton, J.C.D. / Blower, T.R.
History
DepositionJul 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Structure summary / Category: chem_comp_atom / chem_comp_bond / struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF262 domain-containing protein
B: DUF262 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,61710
Polymers135,9782
Non-polymers6398
Water6,305350
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-109 kcal/mol
Surface area52380 Å2
Unit cell
Length a, b, c (Å)214.620, 67.256, 126.547
Angle α, β, γ (deg.)90.000, 102.049, 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 DUF262 domain-containing protein


Mass: 67988.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Plasmid pEFER
Source: (gene. exp.) Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CCUG 18766 / IAM 14443 / JCM 21226 / LMG 7866 / NBRC 102419 / NCTC 12128 / CDC 0568-73) (bacteria)
Strain: ATCC 35469 / DSM 13698 / CCUG 18766 / IAM 14443 / JCM 21226 / LMG 7866 / NBRC 102419 / NCTC 12128 / CDC 0568-73
Gene: EFER_p0024 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7L3S9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.28 Å3/Da / Density % sol: 62.55 % / Description: Crystals formed irregular shards
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris-HCl (pH 7.5), 0.2 M ammonium sulphate, 20% w/v PEG 3350
PH range: 7.4-7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9781 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 2.12→72.89 Å / Num. obs: 99627 / % possible obs: 99.4 % / Redundancy: 2 % / Biso Wilson estimate: 47.35 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.078 / Net I/σ(I): 5.4
Reflection shellResolution: 2.12→2.16 Å / Rmerge(I) obs: 0.899 / Num. unique obs: 4879 / CC1/2: 0.341 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMACCCP4 Program Suite v7.1.015refinement
PHENIX1.14_3260refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.12→72.89 Å / SU ML: 0.3617 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1932 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2515 4928 5.03 %
Rwork0.204 92995 -
obs0.2064 97923 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.55 Å2
Refinement stepCycle: LAST / Resolution: 2.12→72.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9464 0 34 350 9848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00839702
X-RAY DIFFRACTIONf_angle_d0.902913118
X-RAY DIFFRACTIONf_chiral_restr0.05061408
X-RAY DIFFRACTIONf_plane_restr0.00511700
X-RAY DIFFRACTIONf_dihedral_angle_d23.1913612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.140.44341310.39362403X-RAY DIFFRACTION76.39
2.14-2.170.35521550.36822712X-RAY DIFFRACTION84.72
2.17-2.20.36621550.36262916X-RAY DIFFRACTION93.97
2.2-2.220.38661520.36422948X-RAY DIFFRACTION92.98
2.22-2.250.49151520.46763038X-RAY DIFFRACTION95.62
2.25-2.280.35631700.36083066X-RAY DIFFRACTION98.18
2.28-2.320.34131630.30693147X-RAY DIFFRACTION98.54
2.32-2.350.32791540.27823108X-RAY DIFFRACTION98.55
2.35-2.390.32771870.26133127X-RAY DIFFRACTION98.66
2.39-2.430.29181600.2563098X-RAY DIFFRACTION98.82
2.43-2.470.31151630.25383135X-RAY DIFFRACTION98.92
2.47-2.510.32461500.25583164X-RAY DIFFRACTION98.93
2.51-2.560.34981640.2683166X-RAY DIFFRACTION99.02
2.56-2.610.2971740.253112X-RAY DIFFRACTION98.92
2.61-2.670.2751620.24013135X-RAY DIFFRACTION98.92
2.67-2.730.30711650.23073121X-RAY DIFFRACTION99.13
2.73-2.80.24931680.21953182X-RAY DIFFRACTION99.11
2.8-2.880.31271830.22543112X-RAY DIFFRACTION99.34
2.88-2.960.31561690.23543132X-RAY DIFFRACTION99.25
2.96-3.060.28451770.23563175X-RAY DIFFRACTION99.41
3.06-3.170.29861580.22793148X-RAY DIFFRACTION99.34
3.17-3.290.2541610.21673162X-RAY DIFFRACTION99.4
3.29-3.440.28221780.20333169X-RAY DIFFRACTION99.47
3.44-3.620.2051770.19083183X-RAY DIFFRACTION99.64
3.62-3.850.21281850.17153164X-RAY DIFFRACTION99.7
3.85-4.150.22091600.16363197X-RAY DIFFRACTION99.61
4.15-4.570.2071550.15563187X-RAY DIFFRACTION99.67
4.57-5.230.22051620.14933242X-RAY DIFFRACTION99.68
5.23-6.590.22381710.18963238X-RAY DIFFRACTION99.85
6.59-72.890.17121670.15243308X-RAY DIFFRACTION99.03

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