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- PDB-8wcf: Crystal structure of EcThsB -

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Basic information

Entry
Database: PDB / ID: 8wcf
TitleCrystal structure of EcThsB
ComponentsMolecular chaperone Tir
KeywordsHYDROLASE / NAD Hydrolase / anti-phage
Function / homologyThoeris protein ThsB, TIR-like domain superfamily / Thoeris protein ThsB, TIR-like domain / Thoeris protein ThsB, TIR-like domain / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Molecular chaperone Tir
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsChen, Q. / Yu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Self-association activates ThsB NAD + hydrolase for defense against phage infection.
Authors: Luo, Q. / Liu, Q. / Liu, T. / Wang, X. / Wu, X. / Chen, Q. / Yu, Y.
History
DepositionSep 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molecular chaperone Tir
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2093
Polymers18,4501
Non-polymers7592
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.963, 55.712, 58.524
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Molecular chaperone Tir


Mass: 18449.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFSAN025127 / Gene: BANRA_02939 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y8A290
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 46.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) glycerol, 0.1 M Hepes pH 7.0, and 30% (w/v) PEG6000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.299→50 Å / Num. obs: 42082 / % possible obs: 99 % / Redundancy: 12 % / Biso Wilson estimate: 13.05 Å2 / CC1/2: 0.99 / Net I/σ(I): 19.58
Reflection shellResolution: 1.299→1.38 Å / Num. unique obs: 6321 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→38.86 Å / SU ML: 0.107 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.5437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1658 1052 2.5 %
Rwork0.1357 41026 -
obs0.1365 42078 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.72 Å2
Refinement stepCycle: LAST / Resolution: 1.3→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 49 259 1609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561469
X-RAY DIFFRACTIONf_angle_d0.99982009
X-RAY DIFFRACTIONf_chiral_restr0.0714205
X-RAY DIFFRACTIONf_plane_restr0.0043261
X-RAY DIFFRACTIONf_dihedral_angle_d7.0547875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.360.21441210.20344683X-RAY DIFFRACTION91.98
1.36-1.430.19111310.1675108X-RAY DIFFRACTION99.79
1.43-1.520.19151300.1445101X-RAY DIFFRACTION99.98
1.52-1.640.14891320.1265146X-RAY DIFFRACTION100
1.64-1.80.14521320.12175151X-RAY DIFFRACTION99.98
1.8-2.060.13981340.11685192X-RAY DIFFRACTION100
2.06-2.60.18251330.12435223X-RAY DIFFRACTION100
2.6-38.860.16311390.1435422X-RAY DIFFRACTION99.89

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