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- PDB-9cys: Toxin/immunity complex for a T6SS lipase effector from E. cloacae -

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Basic information

Entry
Database: PDB / ID: 9cys
TitleToxin/immunity complex for a T6SS lipase effector from E. cloacae
Components
  • Ankyrin repeat domain-containing protein
  • T6SS lipase effector
KeywordsTOXIN / lipase / immunity / methylglyoxal / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Domain of unknown function DUF3447 / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
CITRIC ACID / methylglyoxal / TRIETHYLENE GLYCOL / ANK_REP_REGION domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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: Nature Communications / Year: 2024
Title: Advanced glycation end-product (AGE) crosslinking activates a type 6 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
DepositionAug 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Ankyrin repeat domain-containing protein
A: T6SS lipase effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9227
Polymers59,3232
Non-polymers5995
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-15 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.081, 111.739, 119.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-611-

HOH

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Components

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Protein , 2 types, 2 molecules IA

#1: Protein Ankyrin repeat domain-containing protein


Mass: 25497.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3CKN4
#2: Protein T6SS lipase effector / Tle


Mass: 33826.016 Da / Num. of mol.: 1 / Fragment: UNP residues 172-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: NCTC10005_04014 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M7ENE2

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Non-polymers , 5 types, 476 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-MIE / methylglyoxal


Mass: 72.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.4 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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→38.12 Å / Num. obs: 66430 / % possible obs: 99.1 % / Redundancy: 7.5 % / Biso Wilson estimate: 33.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Χ2: 1 / Net I/σ(I): 16.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2 / Num. unique obs: 3499 / CC1/2: 0.792 / Rpim(I) all: 0.938 / Rrim(I) all: 0.935 / Χ2: 0.79 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→36.92 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 6644 10.01 %
Rwork0.1829 59755 -
obs0.1858 66399 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.25 Å2 / Biso mean: 38.0526 Å2 / Biso min: 21.4 Å2
Refinement stepCycle: final / Resolution: 1.75→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 38 471 4326
Biso mean--51.02 44.23 -
Num. residues----506
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 (%)
1.75-1.770.48032010.40431910211195
1.77-1.790.32852300.34911920215099
1.79-1.810.37692020.31911987218999
1.81-1.830.3492380.29671945218399
1.83-1.860.30592240.28891909213397
1.86-1.880.31482060.2672026223299
1.88-1.910.26812080.25391983219199
1.91-1.940.28192230.24121945216899
1.94-1.970.24812230.22551968219199
1.97-20.2682240.21781982220699
2-2.040.25092230.21131998222199
2.04-2.070.25322280.22731976220499
2.07-2.110.25962170.2221965218299
2.11-2.160.25112180.209619942212100
2.16-2.20.23962310.21251982221399
2.2-2.250.24912100.20551958216897
2.25-2.310.24172130.19441995220899
2.31-2.370.24492210.206820112232100
2.37-2.440.21212340.18941983221799
2.44-2.520.22592120.192820242236100
2.52-2.610.22742270.194619842211100
2.61-2.720.23192330.193319992232100
2.72-2.840.22092070.194920192226100
2.84-2.990.2022270.18841995222298
2.99-3.180.20732250.184820162241100
3.18-3.420.19852240.172120322256100
3.42-3.760.19162190.160920292248100
3.76-4.310.172260.14212027225398
4.31-5.420.17442290.146620632292100
5.43-36.920.17962410.16382130237199

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