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- PDB-8v6r: Crystal structure of EcThsA in complex with ADPR -

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Basic information

Entry
Database: PDB / ID: 8v6r
TitleCrystal structure of EcThsA in complex with ADPR
ComponentsThoeris protein ThsA Macro domain-containing protein
KeywordsIMMUNE SYSTEM / Antiphage immunity / nucleotide signalling
Function / homologyThoeris protein ThsA, Macro domain / Thoeris protein ThsA, Macro domain / Chem-AR6 / Thoeris protein ThsA Macro domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsShi, Y. / Masic, V. / Mosaiab, T. / Goulart, C.C. / Hartley-Tassell, L. / Sorbello, M. / Vasquez, E. / Mishra, B.P. / Holt, S. / Gu, W. ...Shi, Y. / Masic, V. / Mosaiab, T. / Goulart, C.C. / Hartley-Tassell, L. / Sorbello, M. / Vasquez, E. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7344
Polymers55,6152
Non-polymers1,1192
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-15 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.520, 92.598, 139.976
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: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
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: 2.14→46.66 Å / Num. obs: 29133 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 38.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.05 / Rrim(I) all: 0.111 / Net I/σ(I): 9
Reflection shellResolution: 2.14→2.2 Å / Rmerge(I) obs: 0.969 / Num. unique obs: 2281 / CC1/2: 0.667 / Rpim(I) all: 0.49 / Rrim(I) all: 1.091

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Processing

Software
NameVersionClassification
PHENIX1.18rc3_3805refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→41.67 Å / SU ML: 0.2356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9167
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 1428 4.91 %
Rwork0.205 27632 -
obs0.2065 29060 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.66 Å2
Refinement stepCycle: LAST / Resolution: 2.14→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 72 41 3573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323606
X-RAY DIFFRACTIONf_angle_d0.58614879
X-RAY DIFFRACTIONf_chiral_restr0.0445555
X-RAY DIFFRACTIONf_plane_restr0.0028636
X-RAY DIFFRACTIONf_dihedral_angle_d15.20561360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.220.30531330.28112643X-RAY DIFFRACTION96.52
2.22-2.30.28931430.26412726X-RAY DIFFRACTION99.62
2.3-2.410.2991340.25372696X-RAY DIFFRACTION99.58
2.41-2.540.26821510.22762735X-RAY DIFFRACTION99.59
2.54-2.70.25561330.23352766X-RAY DIFFRACTION99.79
2.7-2.90.27621540.23192741X-RAY DIFFRACTION99.79
2.9-3.20.25881300.23622776X-RAY DIFFRACTION99.62
3.2-3.660.2381520.20992774X-RAY DIFFRACTION99.39
3.66-4.610.20831450.17042825X-RAY DIFFRACTION99.83
4.61-41.670.19261530.17522950X-RAY DIFFRACTION98.85
Refinement TLS params.Method: refined / Origin x: -15.0761647361 Å / Origin y: 19.3239526578 Å / Origin z: -18.4037750662 Å
111213212223313233
T0.253957836016 Å20.0388661925723 Å20.0120671603461 Å2-0.345051579548 Å2-0.00941814093385 Å2--0.327131069183 Å2
L0.684964749588 °20.811773218923 °20.392108133757 °2-4.90695492446 °22.54162137281 °2--3.19728096898 °2
S0.0329124061507 Å °-0.0577828169392 Å °-0.0886768320167 Å °0.660035538555 Å °-0.0461872289209 Å °0.185829587225 Å °0.412230582936 Å °-0.0588319007089 Å °0.00147250826309 Å °
Refinement TLS groupSelection details: all

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