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- PDB-7p9m: BrxU, GmrSD-family Type IV restriction enzyme -

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Basic information

Entry
Database: PDB / ID: 7p9m
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 / GmrSD restriction endonuclease, N-terminal domain / GmrSD restriction endonucleases N-terminal domain-containing protein
Function and homology information
Biological speciesEscherichia fergusonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 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)136,3016
Polymers135,9782
Non-polymers3244
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-83 kcal/mol
Surface area55800 Å2
Unit cell
Length a, b, c (Å)196.875, 68.367, 129.591
Angle α, β, γ (deg.)90.000, 94.448, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
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: 3.2 Å3/Da / Density % sol: 61.53 % / Description: Crystals looked like 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 PEG3350
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→98.14 Å / Num. obs: 40622 / % possible obs: 99.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 98.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.8
Reflection shellResolution: 2.85→2.96 Å / Redundancy: 2 % / Rmerge(I) obs: 1.021 / Num. unique obs: 4514 / CC1/2: 0.368 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMACCCP4 Program Suite v7.1.015refinement
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→98.14 Å / SU ML: 0.6402 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.6959
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2776 1783 4.7 %
Rwork0.2655 36151 -
obs0.2661 37934 93.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.24 Å2
Refinement stepCycle: LAST / Resolution: 2.85→98.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9136 0 16 0 9152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01269339
X-RAY DIFFRACTIONf_angle_d1.89412612
X-RAY DIFFRACTIONf_chiral_restr0.13261364
X-RAY DIFFRACTIONf_plane_restr0.00741633
X-RAY DIFFRACTIONf_dihedral_angle_d17.76353493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.930.4381410.4299849X-RAY DIFFRACTION29.04
2.93-3.010.41621360.42782520X-RAY DIFFRACTION85.13
3.01-3.110.46551360.41132932X-RAY DIFFRACTION99
3.11-3.220.41381200.38852969X-RAY DIFFRACTION99.81
3.22-3.350.39251280.34442975X-RAY DIFFRACTION99.97
3.35-3.50.31371570.3142938X-RAY DIFFRACTION99.94
3.5-3.690.30481450.29082966X-RAY DIFFRACTION99.97
3.69-3.920.27081670.27652957X-RAY DIFFRACTION99.9
3.92-4.220.29971350.25532985X-RAY DIFFRACTION100
4.22-4.640.25471330.23722985X-RAY DIFFRACTION99.97
4.64-5.320.24021890.23772961X-RAY DIFFRACTION100
5.32-6.70.28711680.27352995X-RAY DIFFRACTION100
6.7-98.140.22381280.22233119X-RAY DIFFRACTION99.72

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