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- PDB-8wc0: Crystal structure of EcThsA -

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Basic information

Entry
Database: PDB / ID: 8wc0
TitleCrystal structure of EcThsA
ComponentsNAD(+) hydrolase ThsA
KeywordsHYDROLASE / NAD Hydrolase / anti-phage
Function / homology:
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsChen, Q. / Yu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Self-association activates ThsB NAD+ hydrolase for defense against phage infection
Authors: Chen, Q. / Yu, Y.
History
DepositionSep 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(+) hydrolase ThsA
B: NAD(+) hydrolase ThsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,84711
Polymers110,2792
Non-polymers5689
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-130 kcal/mol
Surface area42140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.640, 250.640, 50.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein NAD(+) hydrolase ThsA


Mass: 55139.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFSAN025127 / Gene: BANRA_02940 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y7ZZJ7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 3.61 Å3/Da / Density % sol: 65.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris Propane pH 8.0, 0.2 M Na2SO4, and 15% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.249→50 Å / Num. obs: 77431 / % possible obs: 99.9 % / Redundancy: 24.4 % / Biso Wilson estimate: 30.16 Å2 / CC1/2: 0.998 / Net I/σ(I): 23.3
Reflection shellResolution: 2.249→2.29 Å / Num. unique obs: 3833 / CC1/2: 0.855

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.249→27.186 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 1161 1.53 %
Rwork0.1883 --
obs0.1889 75831 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.249→27.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7695 0 30 617 8342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047900
X-RAY DIFFRACTIONf_angle_d0.57310679
X-RAY DIFFRACTIONf_dihedral_angle_d4.4276613
X-RAY DIFFRACTIONf_chiral_restr0.041156
X-RAY DIFFRACTIONf_plane_restr0.0031381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.249-2.3510.31931320.30518274X-RAY DIFFRACTION88
2.351-2.47490.28191400.23419117X-RAY DIFFRACTION97
2.4749-2.62990.25551340.21599341X-RAY DIFFRACTION99
2.6299-2.83270.2441470.21569462X-RAY DIFFRACTION100
2.8327-3.11740.19651540.19659427X-RAY DIFFRACTION100
3.1174-3.56770.26151480.18249512X-RAY DIFFRACTION100
3.5677-4.49160.21371490.15019612X-RAY DIFFRACTION100
4.4916-27.1860.18991570.16989925X-RAY DIFFRACTION99

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