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- PDB-7bba: Structure of the TagL peptidoglycan binding domain from EAEC T6SS -

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Basic information

Entry
Database: PDB / ID: 7bba
TitleStructure of the TagL peptidoglycan binding domain from EAEC T6SS
ComponentsPutative type VI secretion protein
KeywordsPROTEIN BINDING / Peptidoglycan binding protein / type VI secretion system
Function / homologyOuter membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / cell outer membrane / Type VI secretion protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsNguyen, V.S. / Cambillau, C. / Leone, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-14-CE14-0006-02 France
CitationJournal: Plos One / Year: 2021
Title: Anchoring the T6SS to the cell wall: Crystal structure of the peptidoglycan binding domain of the TagL accessory protein.
Authors: Nguyen, V.S. / Spinelli, S. / Cascales, E. / Roussel, A. / Cambillau, C. / Leone, P.
History
DepositionDec 17, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionAug 4, 2021ID: 5M3G
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative type VI secretion protein
B: Putative type VI secretion protein
C: Putative type VI secretion protein
D: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,38513
Polymers60,5204
Non-polymers8659
Water3,171176
1
A: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3223
Polymers15,1301
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3223
Polymers15,1301
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4184
Polymers15,1301
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3223
Polymers15,1301
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.890, 75.890, 177.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Putative type VI secretion protein


Mass: 15130.050 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EC042_4528 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 / References: UniProt: D3GUV9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 5.5-6.5 0.6-1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.919762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919762 Å / Relative weight: 1
ReflectionResolution: 2.43→34.9 Å / Num. obs: 21834 / % possible obs: 99.7 % / Redundancy: 21.1 % / Biso Wilson estimate: 72.08 Å2 / CC1/2: 0.991 / Net I/σ(I): 11.7
Reflection shellResolution: 2.43→2.57 Å / Num. unique obs: 3454 / CC1/2: 0.777

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (11-DEC-2020)refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M38

5m38


Resolution: 2.43→34.9 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 0.419 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.413 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.246
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1089 5 %RANDOM
Rwork0.2374 ---
obs0.2378 21796 100 %-
Displacement parametersBiso max: 122.73 Å2 / Biso mean: 75.57 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--7.973 Å20 Å20 Å2
2---7.973 Å20 Å2
3---15.9459 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 2.43→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3463 0 45 176 3684
Biso mean--88.45 64.02 -
Num. residues----449
LS refinement shellResolution: 2.43→2.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.251 21 4.82 %
Rwork0.2257 415 -
all0.2269 436 -
obs--99.78 %

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