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- PDB-7uo8: Co-crystal structure of Salmonella Typhimurium Tlde1a in complex ... -

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Basic information

Entry
Database: PDB / ID: 7uo8
TitleCo-crystal structure of Salmonella Typhimurium Tlde1a in complex with D-methionine
Components
  • HIS-HIS-HIS-HIS-HIS
  • Tlde1a
KeywordsTOXIN / Type VI secretion system / Salmonella Typhimurium / L / D-carboxypeptidase / D-transpeptidase / peptidoglycan
Function / homologyD-METHIONINE / DUF2778 domain-containing protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLorente Cobo, N. / Prehna, G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04968 Canada
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Molecular characterization of the type VI secretion system effector Tlde1a reveals a structurally altered LD-transpeptidase fold.
Authors: Lorente Cobo, N. / Sibinelli-Sousa, S. / Biboy, J. / Vollmer, W. / Bayer-Santos, E. / Prehna, G.
History
DepositionApr 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tlde1a
B: HIS-HIS-HIS-HIS-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5334
Polymers20,2882
Non-polymers2452
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-23 kcal/mol
Surface area9090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.461, 59.461, 106.796
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-996-

HOH

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Components

#1: Protein Tlde1a / SciV protein


Mass: 19440.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct has a His-tag at the carboxy-terminus, but the tag interacts with the active site of a symmetry-related copy of the protein
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: sciV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold / References: UniProt: H9L4J5
#2: Protein/peptide HIS-HIS-HIS-HIS-HIS


Mass: 846.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His-tag from a symmetry-related copy of the Tlde1a construct
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold
#3: Chemical ChemComp-MED / D-METHIONINE


Type: D-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 12mg/ml Tlde1a, 15% PEG 3350, 0.2M Ammonium sulphate, Soaked with 161mM D-methionine for 2 mins 30 secs

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1806 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1806 Å / Relative weight: 1
ReflectionResolution: 1.6→42.05 Å / Num. obs: 26027 / % possible obs: 99.25 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.9
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.449 / Num. unique obs: 2538 / CC1/2: 0.961 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UMA

7uma


Resolution: 1.6→42.05 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 1258 4.87 %
Rwork0.189 24595 -
obs0.1959 26027 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.47 Å2 / Biso mean: 26.5887 Å2 / Biso min: 8.79 Å2
Refinement stepCycle: final / Resolution: 1.6→42.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 24 262 1705
Biso mean--27.27 32.98 -
Num. residues----179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.660.25341350.2388253899.8
1.66-1.740.22211320.21342696100
1.74-1.830.20141540.20132684100
1.83-1.950.34611220.273267098
1.95-2.10.19681460.201265398
2.1-2.310.30051400.227270298
2.31-2.640.16831320.18322734100
2.64-3.330.21291310.17842826100
3.33-42.050.17181660.17172939100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.77322.03080.80026.2621.33414.80020.1864-0.64530.41530.1462-0.2450.0856-0.0216-0.09940.07270.10040.02360.02090.2452-0.08160.111712.582225.65445.0979
22.58533.43682.97286.59074.73436.4473-0.1501-0.40330.4804-0.12780.02340.2713-0.621-0.190.24640.12480.0231-0.00850.1933-0.09580.19788.989929.722942.7229
32.89170.91830.77021.74230.10361.4978-0.15180.32710.0004-0.35230.1092-0.0268-0.0040.1590.03770.1378-0.00860.01660.142-0.00570.058816.820819.652529.2283
45.6159-0.99343.10637.39562.43112.94160.0537-0.8883-0.95070.5045-0.0872-0.6980.75740.69870.02930.26290.0123-0.02290.3810.16310.433821.90048.29445.3094
54.579-0.06621.22613.1014-0.39612.8022-0.00390.0879-0.076-0.1203-0.03850.02770.03920.00550.04650.0764-0.00960.00590.129-0.01170.052512.626119.746532.8913
66.12894.83452.09544.54462.39286.6263-0.38070.09391.5881-0.5486-0.084-0.1099-0.71780.07850.35420.2123-0.0163-0.07450.1556-0.04790.462418.50136.957337.3308
75.77962.0640.76037.2177-1.51423.68670.0563-0.67360.6140.4544-0.3256-0.9991-0.50880.13540.14690.1653-0.016-0.00750.2605-0.07150.173922.751829.014444.7982
82.75290.366-0.82876.2331-1.31184.97710.1504-0.27870.2935-0.0042-0.04840.6468-0.1761-0.156-0.11270.0696-0.0059-0.0130.1877-0.05210.17581.417521.503337.3361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:15)A2 - 15
2X-RAY DIFFRACTION2(chain A and resid 16:24)A16 - 24
3X-RAY DIFFRACTION3(chain A and resid 25:105)A25 - 105
4X-RAY DIFFRACTION4(chain A and resid 106:109)A106 - 109
5X-RAY DIFFRACTION5(chain A and resid 110:138)A110 - 138
6X-RAY DIFFRACTION6(chain A and resid 139:147)A139 - 147
7X-RAY DIFFRACTION7(chain A and resid 148:160)A148 - 160
8X-RAY DIFFRACTION8(chain A and resid 161:175)A161 - 175

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