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Basic information

Entry
Database: PDB / ID: 8ara
TitleHeterologous Complex of Aeromonas hydrophila Type III secretion substrate AscX with Yersinia enterocolitica chaperone YscY
Components
  • AscX
  • Chaperone protein YscY
KeywordsCHAPERONE / Type III Secretion System / T3SS / SctX / SctY
Function / homologyType III secretion system YscX / Type III secretion system chaperone, YscY / Type III secretion system YscX (type_III_YscX) / Tetratricopeptide-like helical domain superfamily / cytoplasm / ACETATE ION / Chaperone protein YscY / AscX
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
Aeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGilzer, D. / Kowal, J.L. / Niemann, H.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: The type III secretion chaperone SctY may shield the hydrophobic export gate-binding C-terminus of its substrate SctX.
Authors: Gilzer, D. / Kowal, J.L. / Flottmann, F. / Niemann, H.H.
History
DepositionAug 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein YscY
B: AscX
C: Chaperone protein YscY
D: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6318
Polymers49,3524
Non-polymers2794
Water1,838102
1
A: Chaperone protein YscY
B: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8635
Polymers24,6762
Non-polymers1873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-38 kcal/mol
Surface area10310 Å2
MethodPISA
2
C: Chaperone protein YscY
D: AscX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7683
Polymers24,6762
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-36 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.318, 94.852, 101.369
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Chaperone protein YscY / / Yop proteins translocation protein Y


Mass: 14077.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: yscY / Plasmid: pACYCDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0C2N2
#2: Protein AscX


Mass: 10598.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GAM remain after TEV cleavage of the N-terminal MBP-tag.
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: ascX / Plasmid: pETM-40 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q699R5

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Non-polymers , 4 types, 106 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: reservoir solution: 0.2 M sodium acetate, 0.1 M sodium citrate pH 5.5, 10 %(w/v) PEG4000; protein: 10 mg/mL in 20 mM Tris pH 8.0, 150 mM NaCl, 5 mM TCEP; drop size: 0.66 uL protein + 0.33 uL reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.3→94.85 Å / Num. obs: 14883 / % possible obs: 75.79 % / Redundancy: 9.4 % / Biso Wilson estimate: 29.21 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.056 / Rrim(I) all: 0.174 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 3 / Num. unique obs: 744 / CC1/2: 0.859 / Rpim(I) all: 0.307 / Rrim(I) all: 0.938 / % possible all: 29

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Processing

Software
NameVersionClassification
XDS20200131data reduction
STARANISO2.3.92 (17-Feb-2023)data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QIH

7qih


Resolution: 2.3→44.7 Å / SU ML: 0.2675 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2426 745 5.02 %
Rwork0.1903 14094 -
obs0.1929 14839 75.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 17 102 2984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282943
X-RAY DIFFRACTIONf_angle_d0.47013975
X-RAY DIFFRACTIONf_chiral_restr0.0309437
X-RAY DIFFRACTIONf_plane_restr0.0029525
X-RAY DIFFRACTIONf_dihedral_angle_d11.62781111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.2656600.23311176X-RAY DIFFRACTION32.12
2.48-2.730.30221050.23061931X-RAY DIFFRACTION53.13
2.73-3.130.2651770.2273376X-RAY DIFFRACTION91.76
3.13-3.940.24321980.18113734X-RAY DIFFRACTION99.97
3.94-44.70.21712050.17183877X-RAY DIFFRACTION99.71
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)
15.371178461371.972958754360.7315515483014.036088762291.67712237383.002455592430.0819448371545-0.7198604588240.667248766261.58916651138-0.100998687942-0.0294922266494-0.0794410584684-0.08890674178650.08608962986680.5899246570370.0804785508978-0.0191388816380.2473401923850.002662712020450.39879145473827.406911311482.128142432986.6296652608
24.656840618911.65438573282-0.6626779313142.927112154080.09839656714162.08540830453-0.0560361197899-0.3631244402850.3709478282560.52185468559-0.0362584986868-0.239618488595-0.3065971238910.382228514918-0.03591770709440.5123896334680.10705910897-0.1222504139250.247499741784-0.07005884449280.3425355273234.365316482374.092008814285.596232286
38.209446876242.939906580552.263650765013.1472286755-1.804801917853.892235441920.033566946048-0.2810745892590.2392453858960.502275281024-0.451955004192-1.07928002436-0.07174504009430.5517221042050.3289432124990.7230628266610.0791839912619-0.2228835103550.3767585294670.05406688776630.57637244717439.013960758964.213741183193.171782984
42.53373677128-1.198588928330.6401655530183.428396085730.1017086251594.6185844155-0.25786835662-0.6603617060050.121070668210.7810618262630.169535550858-0.7219748745130.07392310774160.1568467908830.07565223809160.5722602217140.00329147329104-0.2525728941920.3510913705780.09333942398330.43807857057935.232333278554.264427879297.6124603946
52.76235336035-1.53522624270.2596871872471.83643842969-1.946146359013.325255088450.5218379020410.534555709861-0.265186691143-0.359866587974-0.4411330006920.455207192620.233558387231-0.510869805208-0.119745068140.64130297930.0428562420846-0.1662431838140.4276878407820.03235428897950.32374422517826.800781210455.825558578489.3624914306
69.603311701924.53308857506-2.958451120595.85016121197-1.18001182072.64393637856-0.1015811204210.2971702208090.453270692528-0.08787987643530.0289779159857-0.0330335370746-0.249397160264-0.2212215188980.09441913054830.549750505680.119351771589-0.04783781528610.236247895566-0.08222085159410.31920513485125.827226633587.356771300981.9705885611
78.930068362564.796306194354.542371786648.609027545694.310550870163.636440957080.2972070846750.9029006491640.377684572452-0.004369807632520.327587683589-0.864059150747-0.5010655804440.835098223385-0.445109603910.5955034659190.03688095571930.06601650274410.377806170559-0.004658160540660.58807095843636.936419379185.168051073177.1104576567
82.579811079451.981691293331.621761796835.79747580168-1.061182935792.296647318220.0838525512215-0.7014281740240.9740606055370.366967934583-0.01804774722930.847018306226-1.03901792863-0.53307042148-0.1485066598150.4913258451330.02738765894520.05945171404880.414636144904-0.07807618472630.43096194212417.748628243479.019883589777.4029960572
91.3855525665-0.7071044419630.3920290445582.179575357560.1804612505272.794414031860.0307723095707-0.0736148338539-0.4221280097510.293657184343-0.05889003681140.05402416557070.107156624609-0.2601187600220.0445265627490.256790311889-0.009874539103840.02663685972150.1049320509330.0444638471190.27027815012916.253294963861.577359228765.4925386174
102.24459623364-1.575069465650.5612190311091.63826968289-0.3633060416312.61092914133-0.00679575560540.0691450581587-0.04213144874470.041986303498-0.1378304969820.194211756118-0.3404080915-0.2236815083610.1020437053370.204300523516-0.0136856123184-0.03029920293540.1504232686270.008483999935110.19699088270812.245075157674.216428719955.7868929248
114.714980424522.01712904366-0.2840110581825.33692387088-0.4785000733575.61572331284-0.0663398874931-0.2229526932320.75849811680.498749889876-0.1465815485370.23535156497-0.7139457698240.005906776251580.03763882990960.244881370350.0280422624953-0.07714963471740.140211376688-0.008536369216120.2677764042416.7237279934387.697853293255.9563805856
122.183727314273.15741349594-3.101472093594.85386788471-4.780929136454.717492753770.0595583543113-1.51251884768-0.3279207003271.151676603150.8186761131921.39032961557-1.06699504635-0.279917534091-0.7050042829190.9087131620.327269742630.2052977036611.371371702390.01085719911791.06452228372-4.44556670488.221637846355.405347839
130.749057424787-0.8618921235960.03463090117031.28685104454-0.5424020885052.54690514107-0.13338784762-0.3382118997330.2232686927510.2407031071120.0230607360183-0.1303364107870.1614971152520.428316212941-1.96073241240.871421743448-0.138111594213-0.2812655777810.7006228145830.01023125411260.38429906196610.293760155294.00173795964.6274837252
143.55207432451-3.003957715312.299148440653.24427247312-2.403283975031.78916359855-0.0857910848903-0.5883442499790.1252476478251.29184588598-0.01482123883090.74880292513-0.1089192238770.0774270069467-0.2977217814350.5680559857280.013165719070.07195341579380.352439105555-0.01649313882430.26619555522710.856817579176.184078722669.1619314493
151.63473637592-0.695148153376-1.256874762921.230158998530.7342170880762.93601345648-0.248116784842-0.297188626342-0.7281050729830.151862733887-0.261580727674-0.5293628331131.145054088620.209574343652-0.9192137345430.638246372951-0.0515132713585-0.1226983357560.2139835441190.1111189828810.70248199609220.269739871250.785462860366.7075706236
161.460643346560.0436427173921-0.9970124459363.384768952671.106631068854.48607360024-0.155181437878-0.357602146064-0.2966798963250.6038424261420.179414116845-0.1627662169650.7356989149660.1652805288760.05768700628580.3030647337380.0156155597302-0.06744027673970.2046080934130.08572947146270.37675882328921.871334150859.791288695272.4925830187
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 22 )AA2 - 221 - 21
22chain 'A' and (resid 23 through 59 )AA23 - 5922 - 58
33chain 'A' and (resid 60 through 93 )AA60 - 9359 - 92
44chain 'A' and (resid 94 through 110 )AA94 - 11093 - 109
55chain 'B' and (resid 45 through 60 )BE45 - 601 - 16
66chain 'B' and (resid 61 through 88 )BE61 - 8817 - 34
77chain 'B' and (resid 89 through 104 )BE89 - 10435 - 50
88chain 'B' and (resid 105 through 121 )BE105 - 12151 - 67
99chain 'C' and (resid 3 through 39 )CH3 - 391 - 37
1010chain 'C' and (resid 40 through 93 )CH40 - 9338 - 91
1111chain 'C' and (resid 94 through 109 )CH94 - 10992 - 107
1212chain 'C' and (resid 110 through 114 )CH110 - 114108 - 112
1313chain 'D' and (resid 45 through 49 )DK45 - 491 - 5
1414chain 'D' and (resid 50 through 74 )DK50 - 746 - 20
1515chain 'D' and (resid 75 through 91 )DK75 - 9121 - 37
1616chain 'D' and (resid 92 through 121 )DK92 - 12138 - 67

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