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- PDB-8v6q: Crystal structure of EcThsA in ligand-free state -

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Basic information

Entry
Database: PDB / ID: 8v6q
TitleCrystal structure of EcThsA in ligand-free state
ComponentsThoeris protein ThsA Macro domain-containing protein
KeywordsIMMUNE SYSTEM / Antiphage immunity / nucleotide signalling
Function / homologyThoeris protein ThsA, Macro domain / Thoeris protein ThsA, Macro domain / Thoeris protein ThsA Macro domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsShi, Y. / Masic, V. / Mosaiab, T. / Goulart, C.C. / Hartley-Tassell, L. / Sorbello, M. / Vasquez, V. / Mishra, B.P. / Holt, S. / Gu, W. ...Shi, Y. / Masic, V. / Mosaiab, T. / Goulart, C.C. / Hartley-Tassell, L. / Sorbello, M. / Vasquez, V. / Mishra, B.P. / Holt, S. / Gu, W. / Kobe, B. / Ve, T.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT200100572 Australia
CitationJournal: Sci Adv / Year: 2024
Title: Structural characterization of macro domain-containing Thoeris antiphage defense systems.
Authors: Shi, Y. / Masic, V. / Mosaiab, T. / Rajaratman, P. / Hartley-Tassell, L. / Sorbello, M. / Goulart, C.C. / Vasquez, E. / Mishra, B.P. / Holt, S. / Gu, W. / Kobe, B. / Ve, T.
History
DepositionDec 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thoeris protein ThsA Macro domain-containing protein
B: Thoeris protein ThsA Macro domain-containing protein


Theoretical massNumber of molelcules
Total (without water)55,6152
Polymers55,6152
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-14 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.036, 93.541, 140.541
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Thoeris protein ThsA Macro domain-containing protein


Mass: 27807.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FPI65_12015 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178STJ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14-24% w/v PEG 1000, 0.2 M Lithium sulfate and 0.1 M phosphate-citrate buffer pH 3.8-4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.62→46.85 Å / Num. obs: 16538 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 57.31 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.059 / Rrim(I) all: 0.0155 / Net I/σ(I): 11
Reflection shellResolution: 2.62→2.74 Å / Rmerge(I) obs: 1.501 / Num. unique obs: 1912 / CC1/2: 0.525 / Rpim(I) all: 0.615 / Rrim(I) all: 1.625

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→44.38 Å / SU ML: 0.3078 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2685 821 4.98 %
Rwork0.2412 15656 -
obs0.2427 16477 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.47 Å2
Refinement stepCycle: LAST / Resolution: 2.62→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 0 2 3446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283512
X-RAY DIFFRACTIONf_angle_d0.5294737
X-RAY DIFFRACTIONf_chiral_restr0.0454533
X-RAY DIFFRACTIONf_plane_restr0.0031602
X-RAY DIFFRACTIONf_dihedral_angle_d13.52211296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.790.33711110.3152489X-RAY DIFFRACTION96.91
2.79-30.32011380.29882589X-RAY DIFFRACTION100
3-3.30.28651180.2882607X-RAY DIFFRACTION99.96
3.3-3.780.30091510.25452575X-RAY DIFFRACTION99.93
3.78-4.760.24181500.21452623X-RAY DIFFRACTION99.96
4.76-44.380.24981530.21512773X-RAY DIFFRACTION99.66

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