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- PDB-8s2n: Xenorhabdus bovienii Rhs toxin TreTu complex with TrxA and TriTu ... -

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Basic information

Entry
Database: PDB / ID: 8s2n
TitleXenorhabdus bovienii Rhs toxin TreTu complex with TrxA and TriTu immunity protein
Components
  • Complete genome segment 11/17
  • Immunity Protein TriX
  • Thioredoxin 1
KeywordsTOXIN / ADP-ribosyltransferase / thioredoxin
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm
Similarity search - Function
: / Scabin-like / Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core ...: / Scabin-like / Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / : / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein / Complete genome segment 11/17 / Thioredoxin 1
Similarity search - Component
Biological speciesXenorhabdus bovienii SS-2004 (bacteria)
Escherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsJurenas, D. / Terradot, L.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)F4526.23 Belgium
CitationJournal: Nat Commun / Year: 2024
Title: Thioredoxin 1 moonlights as a chaperone for an interbacterial ADP-ribosyltransferase toxin.
Authors: Dumont, B. / Terradot, L. / Cascales, E. / Van Melderen, L. / Jurenas, D.
History
DepositionFeb 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunity Protein TriX
B: Complete genome segment 11/17
C: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2737
Polymers43,8593
Non-polymers4144
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-32 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.600, 74.600, 190.703
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Immunity Protein TriX


Mass: 16638.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus bovienii SS-2004 (bacteria)
Gene: XBJ1_1304 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3UXR2
#2: Protein Complete genome segment 11/17


Mass: 15317.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus bovienii SS-2004 (bacteria)
Gene: XBJ1_1305 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3UXR3
#3: Protein Thioredoxin 1 / Trx-1


Mass: 11902.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: trxA, fipA, tsnC, b3781, JW5856 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AA25

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Non-polymers , 3 types, 70 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.06 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.02 M Sodium chloride, 0.02 M Sodium acetate pH 4.0, 33 % v/v PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.11→48.38 Å / Num. obs: 32092 / % possible obs: 99.7 % / Redundancy: 26 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.014 / Rrim(I) all: 0.07 / Χ2: 0.93 / Net I/σ(I): 30.9
Reflection shellResolution: 2.11→2.16 Å / Rmerge(I) obs: 1.628 / Mean I/σ(I) obs: 30.9 / Num. unique obs: 2227 / CC1/2: 0.885 / Rpim(I) all: 0.325 / Rrim(I) all: 1.661 / Χ2: 0.81 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHASER1.18_3845phasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→48.38 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2324 1993 6.24 %
Rwork0.1975 29954 -
obs0.1997 31947 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.37 Å2
Refinement stepCycle: LAST / Resolution: 2.11→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 26 66 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633011
X-RAY DIFFRACTIONf_angle_d0.80054063
X-RAY DIFFRACTIONf_chiral_restr0.054443
X-RAY DIFFRACTIONf_plane_restr0.0054526
X-RAY DIFFRACTIONf_dihedral_angle_d16.85911118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.160.30271320.26942009X-RAY DIFFRACTION95.37
2.16-2.220.27911400.25292083X-RAY DIFFRACTION99.6
2.22-2.280.31341390.24872100X-RAY DIFFRACTION99.51
2.28-2.360.31021420.23272102X-RAY DIFFRACTION99.69
2.36-2.440.28661400.2192098X-RAY DIFFRACTION99.64
2.44-2.540.23511410.21982129X-RAY DIFFRACTION99.96
2.54-2.650.26441390.21412120X-RAY DIFFRACTION99.6
2.65-2.790.27461400.22092120X-RAY DIFFRACTION99.82
2.79-2.970.23991430.22912143X-RAY DIFFRACTION99.96
2.97-3.20.24921440.23612149X-RAY DIFFRACTION100
3.2-3.520.26141440.21042158X-RAY DIFFRACTION99.91
3.52-4.030.23091440.18422167X-RAY DIFFRACTION100
4.03-5.070.17871480.15332220X-RAY DIFFRACTION99.96
5.07-48.380.21321570.18812356X-RAY DIFFRACTION99.76
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)
13.09912392473-0.1783198996440.7215482877118.43172937878-1.312936958884.1827043325-0.101015416028-0.457957428347-0.3654451471291.495159128960.3491928017450.2889297214720.2942698168370.604493011088-0.1884879625690.6451984637810.267201146840.0016753655360.708247467575-0.03206186195220.438751840321-55.767067896721.5589600876-31.6580106302
29.78167706624-0.32015439704-1.547322568622.627600095531.047778949878.68143772342-0.876571157717-1.36003720906-0.9517143067722.1343657380.486002647520.6484296254891.12067931171-0.4347623272920.4709555898590.7568004703540.1764155390750.229920320980.7318016790220.1475690884290.724475516405-63.723427667716.0940621898-27.0797633969
34.80071207449-0.538465793372-0.1999578301617.516708797220.8802177753283.48868073718-0.196572402262-0.359039082066-0.05238907820520.3836947767410.675111083338-0.05966300981970.3652632739010.262559729343-0.192613317720.4223293167250.108515932408-0.06821550672050.551970863919-0.09913700743030.341334067171-19.8376671304-5.06381326935-14.0139967228
41.687240252190.5792798094280.002857706713593.75189057470.8165048399143.345766436760.08633150764620.0839049081258-0.08921863786810.3274388150260.225749223704-0.3787870815470.58320974421.08825230061-0.2515476464420.4411499373790.201796176489-0.09855252064020.660565069959-0.0713478106980.457622790713-19.2102302524-11.5689698232-20.3312864767
53.41271794177-1.194173830911.85354295824.605174116431.028790775596.475742803690.152029812186-0.0656548860332-0.6340466156730.3841677056630.06220369527050.06182834324781.052325286440.44336397217-0.2746941097450.5572418024230.109067707315-0.02415243505960.4264058899810.02107985232310.502508893084-27.2862920795-20.0719505278-24.886332157
66.75041765596-5.76671144845-2.86526703476.629252488282.549925754571.545989424250.0382971744998-0.01016684509471.027790884820.1138976399740.356893654694-0.908917603447-0.2939586775780.16791133132-0.2845470302990.565377428390.0942775543192-0.06045966970870.533324344738-0.006135535216350.630587182432-29.96951824482.01364508939-36.8989697947
72.61060919042-2.47470963329-2.335879188784.594032850923.304996663515.372429334710.0245587069862-0.0121897545788-0.0476057305431-0.03343738151510.07155350468770.2518493618720.1095872344910.0988639332898-0.07793142946040.3470743935170.0480973729824-0.06294496388180.3965487079110.005349065709350.476587474959-31.9198678764-5.76799256758-33.0229401008
86.571195146431.4489280566-0.1437387747866.51507726710.7037235604674.989765950990.2600403404430.587657861272-0.0941004282777-0.833031353351-0.2472916053640.5407194145350.226718979445-0.6006577764450.006710191940630.363283942850.0923284748202-0.08480887169540.460311564731-0.03842470166680.374025390804-33.34553649-10.3926454469-42.1201905439
94.22268869182-5.382581245433.404179494189.27080481142-3.027501931063.800343455310.175053637646-0.08413653042370.494163280411-0.2000896598990.284771338739-0.089737135735-0.219498800642-0.594034933576-0.3502982939190.4728400134610.100891600658-0.01845686662070.498836878665-0.07414431129250.59102406359-39.99602797218.27594809458-31.8160390206
103.793269771811.57890108460.2575543236986.59865444879-0.2655905955995.75420473508-0.2804527315350.113144168020.0967160471639-0.4141007529210.1487512307490.06174834264740.06294673061320.2333928802720.07546945709420.4313915874460.1722151496370.01333929593780.596018071391-0.1709633021590.45319648022-57.777113419218.0634482902-47.0009364181
110.9136230876822.17261612906-0.7654481737618.519326067460.1357926098932.157701267850.2174156797150.637880636098-0.266860279765-0.5287865910410.03239563565970.730813419735-0.672365891552-0.197788262683-0.03188845043560.4127400832510.161646469995-0.04036514559480.607904495068-0.08922552059280.537351399564-57.688830154928.297749805-43.1526127541
129.09851426719-3.72999028733-3.154764695753.104250857663.096839536584.93870375205-0.451984576338-0.273454116728-0.7379110218190.9262610566780.2558075927920.09338768461311.087177450170.3772341891180.3012447115310.6595368607290.248623061645-0.06696318840350.628851922114-0.06459332397390.647085657638-51.586048291213.0671682537-39.1209172941
139.32775118224-3.673038167211.999213553898.50741972924-0.3935698931079.36146406551-0.0640091441707-0.0682311776711-2.823425903090.2503786709750.3244518657261.162562802542.17866578941-0.4179189306-0.03148311247490.962973331889-0.06096709148060.1361617169570.473598742839-0.01083866893890.780130807988-60.63749529278.75254506574-36.4710448004
144.35989409690.578359797231-1.104756816466.104399376420.6450607590244.48876500603-0.128084097326-0.3753056649940.2049205512930.1777608978040.281169904985-0.225208638170.3387789933060.502906611915-0.1820337218950.5111701817550.232212570191-0.08454630415640.557073390006-0.06432751917160.394458427621-56.724428101117.3462592954-41.2731170257
155.48437613317-1.962164208420.5356829589893.49514229028-5.04026031438.44123551828-0.273558009303-0.1753551051560.3588626505441.12945794015-0.388428232532-1.25248327977-0.2918782955151.172702797030.6589554325430.5040565773820.148231567262-0.1521064021540.661276513123-0.07157007060370.622084798441-45.358621697620.5355869063-35.8072207611
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 80 through 98 )CE80 - 9877 - 95
22chain 'C' and (resid 99 through 110 )CE99 - 11096 - 107
33chain 'A' and (resid 1 through 38 )AA1 - 381 - 38
44chain 'A' and (resid 39 through 85 )AA39 - 8539 - 85
55chain 'A' and (resid 86 through 135 )AA86 - 13586 - 135
66chain 'B' and (resid 10 through 38 )BD10 - 381 - 29
77chain 'B' and (resid 39 through 82 )BD39 - 8230 - 73
88chain 'B' and (resid 83 through 111 )BD83 - 11174 - 102
99chain 'B' and (resid 112 through 139 )BD112 - 139103 - 130
1010chain 'C' and (resid 4 through 14 )CE4 - 141 - 11
1111chain 'C' and (resid 15 through 25 )CE15 - 2512 - 22
1212chain 'C' and (resid 26 through 35 )CE26 - 3523 - 32
1313chain 'C' and (resid 36 through 51 )CE36 - 5133 - 48
1414chain 'C' and (resid 52 through 68 )CE52 - 6849 - 65
1515chain 'C' and (resid 69 through 79 )CE69 - 7966 - 76

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