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- PDB-7uo3: Co-crystal structure of Salmonella Typhimurium Tlde1a in complex ... -

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Basic information

Entry
Database: PDB / ID: 7uo3
TitleCo-crystal structure of Salmonella Typhimurium Tlde1a in complex with D-alanine
Components
  • HIS-HIS-HIS-HIS
  • Tlde1a
KeywordsTOXIN / Type VI secretion system / Salmonella Typhimurium / L / D-carboxypeptidase / D-transpeptidase / peptidoglycan
Function / homologyD-ALANINE / 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: 1.8 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 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9818
Polymers20,4192
Non-polymers5626
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-69 kcal/mol
Surface area9090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.140, 60.140, 105.699
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-1137-

HOH

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Components

#1: Protein Tlde1a / Murein L / D-transpeptidase / SciV protein


Mass: 19442.916 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


Mass: 976.010 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-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 12mg/ml Tlde1a, 15% PEG 3350, 0.2M Ammonium sulphate, Soaked with 300mM D-alanine for 2 mins

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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: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1806 Å / Relative weight: 1
ReflectionResolution: 1.8→42.53 Å / Num. obs: 18721 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.993 / Rmerge(I) obs: 0.185 / Net I/σ(I): 9.1
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.693 / Num. unique obs: 1081 / CC1/2: 0.343

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UMA

7uma


Resolution: 1.8→39.7 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 910 4.88 %
Rwork0.1732 17754 -
obs0.1749 18664 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.09 Å2 / Biso mean: 41.5694 Å2 / Biso min: 19.28 Å2
Refinement stepCycle: final / Resolution: 1.8→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 44 174 1625
Biso mean--58.53 40.69 -
Num. residues----178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.890.33671240.298824802604
1.89-2.010.28341230.247324822605
2.01-2.170.23091400.17924732613
2.17-2.390.20121330.166125092642
2.39-2.730.20731070.180525402647
2.73-3.440.22911330.167325572690
3.44-39.70.17731500.153927132863
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)
19.15162.4593-1.41178.4864-0.3228.06620.0936-0.36760.3550.2797-0.1669-0.2258-0.52130.17070.08630.24330.0168-0.00310.2047-0.01530.182214.508826.356745.6204
24.82593.90173.58723.33842.5293.03180.0558-0.17220.2926-0.1815-0.27180.2171-0.2671-0.38780.25330.24750.00260.01160.240.01240.21528.691726.300840.2743
34.661-0.81810.06983.450.58743.247-0.02530.0238-0.4029-0.1450.07730.1338-0.0223-0.0819-0.04390.2243-0.0327-0.03050.20970.01320.27127.255710.322536.0739
43.42970.36740.35655.1301-4.91774.83440.03880.14810.1165-0.0085-0.3568-0.6119-0.1580.7780.41460.2919-0.03780.01170.3608-0.0210.293724.056624.139837.1997
54.84175.50475.14716.73325.57175.64390.12610.3942-0.3164-0.6708-0.3173-0.80040.10380.85870.07950.53140.00830.06980.83240.0090.356622.415121.260817.2881
65.03380.63223.61852.0537-0.00574.4554-0.19330.92910.11-0.31590.0369-0.0243-0.11960.65660.10860.2485-0.0510.0440.44950.04510.306920.247425.004422.3824
74.56262.04692.64074.03143.24325.4804-0.1790.68890.1389-0.61690.15440.1149-0.26920.29990.08830.328-0.05910.01050.36660.06210.247811.949423.461618.9815
84.94950.33011.92492.466-1.82594.42790.2243-0.1196-0.6902-0.0329-0.0926-0.0770.43180.363-0.21370.23320.0562-0.00390.2198-0.03320.258921.623613.879938.3336
94.1462-0.2581.48011.05880.41783.6130.05360.2237-0.1666-0.20480.0033-0.02150.1232-0.0244-0.06170.218-0.01180.00120.25960.00740.229612.027920.028331.2053
107.5453.04793.11887.03643.26746.5216-0.06620.2550.8027-0.31350.0220.0651-0.48770.29860.16130.3172-0.0259-0.02640.2210.03280.315916.274435.83837.1378
118.60713.5235-0.33913.1011-3.10895.40570.2365-0.14980.58690.9338-0.3219-0.4386-0.87960.70770.12290.3323-0.0685-0.01870.3473-0.04480.326724.285131.544842.9219
125.199-1.32361.66664.4714-1.7553.8160.1879-0.40380.02310.07320.04850.26630.0529-0.0714-0.30080.2149-0.0158-0.01340.2794-0.04410.21882.847519.894138.9888
134.7792-2.39454.41346.1996-1.95234.08630.53012.0551-0.5818-1.4904-0.7693-0.00462.23682.0608-0.0840.95710.02730.13990.6909-0.06740.442417.208313.21524.2462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )A1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 27 )A16 - 27
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 45 )A28 - 45
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 55 )A46 - 55
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 65 )A56 - 65
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 83 )A66 - 83
7X-RAY DIFFRACTION7chain 'A' and (resid 84 through 95 )A84 - 95
8X-RAY DIFFRACTION8chain 'A' and (resid 96 through 113 )A96 - 113
9X-RAY DIFFRACTION9chain 'A' and (resid 114 through 135 )A114 - 135
10X-RAY DIFFRACTION10chain 'A' and (resid 136 through 146 )A136 - 146
11X-RAY DIFFRACTION11chain 'A' and (resid 147 through 159 )A147 - 159
12X-RAY DIFFRACTION12chain 'A' and (resid 160 through 174 )A160 - 174
13X-RAY DIFFRACTION13chain 'B' and (resid 301 through 304 )B301 - 304

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