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- PDB-8boz: structure of the Adherent-Invasive Escherichia coli Tle3/Tli3 T6S... -

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Basic information

Entry
Database: PDB / ID: 8boz
Titlestructure of the Adherent-Invasive Escherichia coli Tle3/Tli3 T6SS effector/immunity complex
Components
  • Lipoprotein
  • Transmembrane protein
KeywordsHYDROLASE / Phospholipase / immunity / adherent-invasive Escherichia coli (AIEC) / / protein secretion / Protein structure / AlphaFold2
Function / homologyAlpha/Beta hydrolase fold / Lipoprotein / Transmembrane protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsCambillau, C. / Roussel, A.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Int J Mol Sci / Year: 2023
Title: Activity and Crystal Structure of the Adherent-Invasive Escherichia coli Tle3/Tli3 T6SS Effector/Immunity Complex Determined Using an AlphaFold2 Predicted Model.
Authors: Le, T.T.H. / Kellenberger, C. / Boyer, M. / Santucci, P. / Flaugnatti, N. / Cascales, E. / Roussel, A. / Canaan, S. / Journet, L. / Cambillau, C.
History
DepositionNov 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane protein
C: Transmembrane protein
B: Lipoprotein
E: Transmembrane protein
D: Lipoprotein
F: Lipoprotein
G: Transmembrane protein
H: Lipoprotein
I: Transmembrane protein
J: Lipoprotein
K: Transmembrane protein
L: Lipoprotein
M: Transmembrane protein
N: Lipoprotein
O: Transmembrane protein
P: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)837,56124
Polymers837,24016
Non-polymers3218
Water00
1
A: Transmembrane protein
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6953
Polymers104,6552
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-6 kcal/mol
Surface area30750 Å2
MethodPISA
2
C: Transmembrane protein
D: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6953
Polymers104,6552
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-20 kcal/mol
Surface area29860 Å2
MethodPISA
3
E: Transmembrane protein
F: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6953
Polymers104,6552
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-23 kcal/mol
Surface area31530 Å2
MethodPISA
4
G: Transmembrane protein
H: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6953
Polymers104,6552
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-25 kcal/mol
Surface area31570 Å2
MethodPISA
5
I: Transmembrane protein
J: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6953
Polymers104,6552
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-25 kcal/mol
Surface area31060 Å2
MethodPISA
6
K: Transmembrane protein
L: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6953
Polymers104,6552
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-25 kcal/mol
Surface area30360 Å2
MethodPISA
7
M: Transmembrane protein
N: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6953
Polymers104,6552
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-23 kcal/mol
Surface area30200 Å2
MethodPISA
8
O: Transmembrane protein
P: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6953
Polymers104,6552
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-20 kcal/mol
Surface area30590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.860, 449.070, 116.230
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transmembrane protein


Mass: 73992.266 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FPI65_17315 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G9AAY6
#2: Protein
Lipoprotein


Mass: 30662.744 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FPI65_17310 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G9AAX8
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Tle3AIEC-Tli3AIEC crystals were obtained using a reservoir solution consisting of 20% v/v PEG 3350. Bis Tris propane pH 6.5, 0.2 M sodium acetate trihydrate after 44 days at 293 K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.6→48.75 Å / Num. obs: 78970 / % possible obs: 98.9 % / Redundancy: 3.9 % / CC1/2: 0.976 / Net I/σ(I): 4.5
Reflection shellResolution: 3.6→3.64 Å / Num. unique obs: 5814 / CC1/2: 0.383

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 3.6→48.74 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 3949 5 %
Rwork0.2326 --
obs0.2344 78957 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45226 0 8 0 45234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00346454
X-RAY DIFFRACTIONf_angle_d0.59163537
X-RAY DIFFRACTIONf_dihedral_angle_d4.5526519
X-RAY DIFFRACTIONf_chiral_restr0.0416858
X-RAY DIFFRACTIONf_plane_restr0.0058441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.640.37581400.34052660X-RAY DIFFRACTION99
3.64-3.690.36631390.31162643X-RAY DIFFRACTION99
3.69-3.740.33961460.30522761X-RAY DIFFRACTION99
3.74-3.790.35851400.30682665X-RAY DIFFRACTION99
3.79-3.840.31871390.27842651X-RAY DIFFRACTION99
3.84-3.90.30241410.28222665X-RAY DIFFRACTION99
3.9-3.960.32451430.28132717X-RAY DIFFRACTION99
3.96-4.030.31061400.26792675X-RAY DIFFRACTION99
4.03-4.10.31561410.25912671X-RAY DIFFRACTION99
4.1-4.170.30441420.24692703X-RAY DIFFRACTION99
4.17-4.250.27961420.2362699X-RAY DIFFRACTION99
4.25-4.340.26731400.24112642X-RAY DIFFRACTION99
4.34-4.430.28741400.22822677X-RAY DIFFRACTION99
4.43-4.530.27221440.22712736X-RAY DIFFRACTION99
4.53-4.650.30471390.22792636X-RAY DIFFRACTION99
4.65-4.770.26261420.21732698X-RAY DIFFRACTION99
4.77-4.910.25981410.21772670X-RAY DIFFRACTION99
4.91-5.070.24321420.21852704X-RAY DIFFRACTION100
5.07-5.250.26161430.22322707X-RAY DIFFRACTION99
5.25-5.460.28191400.22682667X-RAY DIFFRACTION100
5.46-5.710.24631430.22752707X-RAY DIFFRACTION99
5.71-6.010.29921400.22752671X-RAY DIFFRACTION99
6.01-6.390.27351410.22472666X-RAY DIFFRACTION99
6.39-6.880.24171420.21372714X-RAY DIFFRACTION99
6.88-7.570.22131410.20242668X-RAY DIFFRACTION98
7.57-8.660.21511400.18862657X-RAY DIFFRACTION98
8.66-10.890.19241390.17972657X-RAY DIFFRACTION98
10.9-48.740.24761390.24062621X-RAY DIFFRACTION96

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