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- PDB-8xcl: Character of TseP: a dual functional effector of type VI secretio... -

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Basic information

Entry
Database: PDB / ID: 8xcl
TitleCharacter of TseP: a dual functional effector of type VI secretion system
ComponentsEF-hand domain-containing protein
KeywordsHYDROLASE / T6SS / interspecies interaction / bifunctional effector / peptidoglycan hydrolysis
Function / homologyEF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Lysozyme-like domain superfamily / calcium ion binding / EF-hand domain-containing protein
Function and homology information
Biological speciesAeromonas dhakensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsQin, W.M. / Zhao, T. / Dong, T. / Wang, Z.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Elife / Year: 2025
Title: Amidase and lysozyme dual functions in TseP reveal a new family of chimeric effectors in the type VI secretion system.
Authors: Wang, Z.H. / An, Y. / Zhao, T. / Pei, T.T. / Wang, D.Y. / Liang, X. / Qin, W. / Dong, T.
History
DepositionDec 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EF-hand domain-containing protein


Theoretical massNumber of molelcules
Total (without water)27,2581
Polymers27,2581
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.481, 138.797, 95.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-421-

HOH

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Components

#1: Protein EF-hand domain-containing protein / TseP


Mass: 27257.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas dhakensis (bacteria) / Gene: HMPREF1171_00947 / Production host: Escherichia coli (E. coli) / References: UniProt: K1JFN7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium formate pH 7.0 ,12% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.26→48.1 Å / Num. obs: 25776 / % possible obs: 95.9 % / Redundancy: 12.9 % / CC1/2: 0.984 / Rmerge(I) obs: 0.218 / Rrim(I) all: 0.236 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.26-2.40.77143040.840.8361
2.4-2.560.54641000.9190.5891
2.56-2.770.3937900.9550.4221
2.77-3.030.30634870.9630.3311
3.03-3.390.22630280.9740.2441
3.39-3.910.17220400.980.1881
3.91-4.780.14721680.980.161
4.78-6.720.14518290.9810.1571

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.27→47.914 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 708 5.01 %
Rwork0.1869 --
obs0.1889 14135 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→47.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 0 123 2033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071956
X-RAY DIFFRACTIONf_angle_d0.8712638
X-RAY DIFFRACTIONf_dihedral_angle_d6.1351161
X-RAY DIFFRACTIONf_chiral_restr0.05272
X-RAY DIFFRACTIONf_plane_restr0.005345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.4450.25941380.20522623X-RAY DIFFRACTION100
2.445-2.69110.25721390.19122642X-RAY DIFFRACTION100
2.6911-3.08040.24411400.19322654X-RAY DIFFRACTION100
3.0804-3.88070.22171420.17662706X-RAY DIFFRACTION100
3.8807-47.90.20731490.18592802X-RAY DIFFRACTION100

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