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- PDB-7ubz: Chymotrypsin digested toxin/immunity complex for a T6SS lipase ef... -

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Basic information

Entry
Database: PDB / ID: 7ubz
TitleChymotrypsin digested toxin/immunity complex for a T6SS lipase effector from E. cloacae
Components
  • Ankyrin repeat domain-containing protein
  • T6SS lipase effector
KeywordsTOXIN/IMMUNE SYSTEM / lipase / toxin / immunity / methylglyoxal / TOXIN-IMMUNE SYSTEM complex
Function / homologyAlpha/Beta hydrolase fold / CITRATE ANION / methylglyoxal / Phospholipase / :
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCuthbert, B.J. / Jensen, S.J. / Goulding, C.W. / Hayes, C.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)GM117930 United States
CitationJournal: Nat Commun / Year: 2024
Title: Advanced glycation end-product crosslinking activates a type VI secretion system phospholipase effector protein.
Authors: Jensen, S.J. / Cuthbert, B.J. / Garza-Sanchez, F. / Helou, C.C. / de Miranda, R. / Goulding, C.W. / Hayes, C.S.
History
DepositionMar 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin repeat domain-containing protein
C: Ankyrin repeat domain-containing protein
B: T6SS lipase effector
D: T6SS lipase effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,80816
Polymers118,6464
Non-polymers1,16212
Water20,3571130
1
A: Ankyrin repeat domain-containing protein
B: T6SS lipase effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9489
Polymers59,3232
Non-polymers6257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-17 kcal/mol
Surface area18990 Å2
MethodPISA
2
C: Ankyrin repeat domain-containing protein
D: T6SS lipase effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8617
Polymers59,3232
Non-polymers5375
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-19 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.172, 120.493, 122.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Ankyrin repeat domain-containing protein / Immunity protein / Tli


Mass: 25497.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: I6L61_16350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8F3KJ65
#2: Protein T6SS lipase effector / Tle


Mass: 33826.016 Da / Num. of mol.: 2 / Fragment: UNP residues 172-472
Source method: isolated from a genetically manipulated source
Details: Treated with chymotrypsin during crystallization / Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: NCTC10005_04014 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M7ENE2

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Non-polymers , 4 types, 1142 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-MIE / methylglyoxal


Mass: 72.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1130 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.25 M sodium citrate, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.75→38.88 Å / Num. obs: 130201 / % possible obs: 99.1 % / Redundancy: 37.1 % / Biso Wilson estimate: 28.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.02 / Rrim(I) all: 0.121 / Net I/σ(I): 23.2 / Num. measured all: 4829779 / Scaling rejects: 2012
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 29.3 % / Rmerge(I) obs: 2.725 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5526 / CC1/2: 0.733 / Rpim(I) all: 0.497 / Rrim(I) all: 2.772 / % possible all: 85.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7UC0

7uc0
PDB Unreleased entry


Resolution: 1.75→38.76 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1882 13008 10 %
Rwork0.1642 117034 -
obs0.1666 130042 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.18 Å2 / Biso mean: 33.335 Å2 / Biso min: 15.07 Å2
Refinement stepCycle: final / Resolution: 1.75→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6500 0 73 1130 7703
Biso mean--57.75 42.61 -
Num. residues----853
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.40623570.36973160351781
1.77-1.790.33574000.29893709410995
1.79-1.810.2854400.27213854429499
1.81-1.830.29834310.244538954326100
1.83-1.860.27044280.222939454373100
1.86-1.880.25634400.21338514291100
1.88-1.910.23784300.197139274357100
1.91-1.940.20574360.188938744310100
1.94-1.970.21694300.18239004330100
1.97-20.21414350.183839034338100
2-2.030.22724270.180739374364100
2.03-2.070.21244270.18063830425798
2.07-2.110.20694360.18238904326100
2.11-2.150.23264430.181239454388100
2.15-2.20.19914350.175138844319100
2.2-2.250.20364490.167539164365100
2.25-2.310.20184200.162839394359100
2.31-2.370.1944430.163139304373100
2.37-2.440.21084450.165539214366100
2.44-2.520.19634210.16533876429799
2.52-2.610.19184430.164339634406100
2.61-2.710.18244380.166539124350100
2.71-2.840.19164330.169739514384100
2.84-2.990.19794400.164739584398100
2.99-3.170.18824470.160939624409100
3.17-3.420.17714380.1563955439399
3.42-3.760.16624390.147339864425100
3.76-4.30.1484490.135340164465100
4.31-5.420.15684460.13540544500100
5.42-38.760.16794620.16384191465399

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