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- PDB-8qjd: T6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core domain -

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Basic information

Entry
Database: PDB / ID: 8qjd
TitleT6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core domain
ComponentsSalmonella bongori Rhs core domain (residues 360-1420)
KeywordsCELL INVASION / Rhs / T6SS / PAAR-Rhs / toxin cannister / Rhs-repeat
Function / homology
Function and homology information


Tox-PAAR-like domain / Toxin PAAR-like domain / Domain of unknown function DUF6531 / Domain of unknown function (DUF6531) / RHS protein / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / :
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesSalmonella bongori N268-08 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.203 Å
AuthorsKielkopf, C.S. / Shneider, M.M. / Leiman, P.G. / Taylor, N.M.I.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_144243 Switzerland
CitationJournal: Structure / Year: 2024
Title: T6SS-associated Rhs toxin-encapsulating shells: Structural and bioinformatical insights into bacterial weaponry and self-protection.
Authors: Kielkopf, C.S. / Shneider, M.M. / Leiman, P.G. / Taylor, N.M.I.
History
DepositionSep 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Salmonella bongori Rhs core domain (residues 360-1420)
B: Salmonella bongori Rhs core domain (residues 360-1420)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,5324
Polymers245,4012
Non-polymers1312
Water21,7801209
1
A: Salmonella bongori Rhs core domain (residues 360-1420)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7662
Polymers122,7001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Salmonella bongori Rhs core domain (residues 360-1420)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7662
Polymers122,7001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.071, 118.260, 131.757
Angle α, β, γ (deg.)90.000, 105.520, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 360 through 532 or resid 534...
d_2ens_1(chain "B" and (resid 360 through 532 or resid 534...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUGLNGLNAA360 - 5325 - 177
d_12GLNGLNASPASPAA534 - 773179 - 418
d_13LEULEUSERSERAA775 - 794420 - 439
d_14ASNASNMETMETAA796 - 817441 - 462
d_15GLNGLNSERSERAA819 - 940464 - 585
d_16VALVALLEULEUAA943 - 1050588 - 695
d_17GLNGLNHISHISAA1052 - 1174697 - 819
d_18VALVALVALVALAA1192837
d_19VALVALILEILEAA1194 - 1195839 - 840
d_110ASPASPILEILEAA1197 - 1215842 - 860
d_111PROPROTYRTYRAA1222 - 1227867 - 872
d_112TRPTRPGLUGLUAA1229 - 1244874 - 889
d_113ARGARGILEILEAA1246 - 1296891 - 941
d_114TRPTRPGLYGLYAA1298 - 1351943 - 996
d_115ASNASNLEULEUAA1353 - 1420998 - 1065
d_21GLUGLUGLNGLNBB360 - 5325 - 177
d_22GLNGLNASPASPBB534 - 773179 - 418
d_23LEULEUSERSERBB775 - 794420 - 439
d_24ASNASNMETMETBB796 - 817441 - 462
d_25GLNGLNSERSERBB819 - 940464 - 585
d_26VALVALLEULEUBB943 - 1050588 - 695
d_27GLNGLNGLYGLYBB1052 - 1066697 - 711
d_28ASNASNHISHISBB1078 - 1174723 - 819
d_29VALVALVALVALBB1192837
d_210VALVALILEILEBB1194 - 1195839 - 840
d_211ASPASPILEILEBB1197 - 1215842 - 860
d_212PROPROTYRTYRBB1222 - 1227867 - 872
d_213TRPTRPGLUGLUBB1229 - 1244874 - 889
d_214ARGARGILEILEBB1246 - 1296891 - 941
d_215TRPTRPGLYGLYBB1298 - 1351943 - 996
d_216ASNASNLEULEUBB1353 - 1420998 - 1065

NCS oper: (Code: givenMatrix: (-0.990952459873, -0.047341981055, 0.125586460664), (-0.0515359208119, 0.998209648747, -0.030356976384), (-0.123924457386, -0.0365545343139, -0.991618119481)Vector: -12. ...NCS oper: (Code: given
Matrix: (-0.990952459873, -0.047341981055, 0.125586460664), (-0.0515359208119, 0.998209648747, -0.030356976384), (-0.123924457386, -0.0365545343139, -0.991618119481)
Vector: -12.0638572627, 62.1759701781, 186.919737192)

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Components

#1: Protein Salmonella bongori Rhs core domain (residues 360-1420)


Mass: 122700.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella bongori N268-08 (bacteria) / Gene: A464_2174 / Production host: Escherichia coli B (bacteria) / References: UniProt: S5MXP0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1209 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein was diluted to 3 mg/ml using MonoQ buffer A and 1 ul was mixed with 2 ul of reservoir solution (0.1 M MES pH 7, 20% PEE 270, 3.67% acetone) in a hanging drop vapor diffusion ...Details: Protein was diluted to 3 mg/ml using MonoQ buffer A and 1 ul was mixed with 2 ul of reservoir solution (0.1 M MES pH 7, 20% PEE 270, 3.67% acetone) in a hanging drop vapor diffusion experiment at 19 deg C to obtain the crystals for the native dataset used for SIRAS phasing and for refinement. Before the diffraction experiment, crystals were cryoprotected by soaking in a solution consisting of 0.1M MES pH7 and 35% PEE270. For the Hg(II) derivative dataset used in SIRAS phasing, the crystal was grown in a similar fashion but using a reservoir solution comprising 0.1 M HEPES pH 7, 20% PEE 270. Derivatisation was performed by soaking the crystal for a couple of minutes in reservoir solution supplemented with 12.5 mM thimerosal. Crystals were back soaked and cryoprotected in mother liquor with an increased PEE 270 concentration (35%).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.203→49.17 Å / Num. obs: 147230 / % possible obs: 99.61 % / Redundancy: 6.84 % / Biso Wilson estimate: 37.86 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08007 / Rpim(I) all: 0.03298 / Rrim(I) all: 0.08671 / Net I/σ(I): 17.62
Reflection shellResolution: 2.203→2.281 Å / Rmerge(I) obs: 0.8547 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 14230 / CC1/2: 0.836 / CC star: 0.954 / Rrim(I) all: 0.9292 / % possible all: 97.11

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487+SVNrefinement
PHENIX1.18.2_3874refinement
Coot0.9.3model building
ARP/wARPmodel building
BUCCANEERphasing
SHARPphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.203→49.17 Å / SU ML: 0.2711 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.0092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.211 14502 5.01 %
Rwork0.1822 274927 -
obs0.1837 147188 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.95 Å2
Refinement stepCycle: LAST / Resolution: 2.203→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16859 0 2 1209 18070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003617259
X-RAY DIFFRACTIONf_angle_d0.665623430
X-RAY DIFFRACTIONf_chiral_restr0.04612438
X-RAY DIFFRACTIONf_plane_restr0.00553111
X-RAY DIFFRACTIONf_dihedral_angle_d12.82216360
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.412648743443 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.203-2.230.40044220.36778146X-RAY DIFFRACTION88.43
2.23-2.250.34544900.29359170X-RAY DIFFRACTION99.81
2.25-2.280.30754800.28519164X-RAY DIFFRACTION99.79
2.28-2.310.32534970.27479383X-RAY DIFFRACTION99.76
2.31-2.340.28884790.26439065X-RAY DIFFRACTION99.77
2.34-2.370.30874910.25479289X-RAY DIFFRACTION99.7
2.37-2.410.2784830.23889211X-RAY DIFFRACTION99.73
2.41-2.440.28994810.23839136X-RAY DIFFRACTION99.78
2.44-2.480.25754900.22729240X-RAY DIFFRACTION99.73
2.48-2.520.23784810.21699167X-RAY DIFFRACTION99.78
2.52-2.560.24424840.21789247X-RAY DIFFRACTION99.77
2.56-2.610.2684860.20989206X-RAY DIFFRACTION99.74
2.61-2.660.23764830.20069146X-RAY DIFFRACTION99.78
2.66-2.720.24054860.20189234X-RAY DIFFRACTION99.76
2.72-2.780.2694850.20689191X-RAY DIFFRACTION99.73
2.78-2.840.25854920.20549240X-RAY DIFFRACTION99.6
2.84-2.910.25374850.19919218X-RAY DIFFRACTION99.58
2.91-2.990.22164830.19429159X-RAY DIFFRACTION99.57
2.99-3.080.23524890.19049204X-RAY DIFFRACTION99.71
3.08-3.180.22424850.19189180X-RAY DIFFRACTION99.71
3.18-3.290.234860.18769229X-RAY DIFFRACTION99.59
3.29-3.420.20954840.18579191X-RAY DIFFRACTION99.69
3.42-3.580.21094880.16689154X-RAY DIFFRACTION99.67
3.58-3.770.18264880.15269218X-RAY DIFFRACTION99.43
3.77-40.17254790.15169193X-RAY DIFFRACTION99.65
4-4.310.15714870.1439221X-RAY DIFFRACTION99.61
4.31-4.740.14144850.12779183X-RAY DIFFRACTION99.64
4.74-5.430.15984860.14439189X-RAY DIFFRACTION99.73
5.43-6.840.20094830.17039218X-RAY DIFFRACTION99.8
6.84-49.170.18154840.17869135X-RAY DIFFRACTION99.13
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)
10.459217637345-0.215477152713-0.2742070794571.82746133330.02453090497110.724895889985-0.01532682098720.02633852797530.0253492739126-0.1250382334040.0738971851811-0.320783275009-0.04880046403910.289045168824-0.05905409156030.561811910975-0.046445085681-0.02566088109760.376969330545-0.01992755532210.3068610016442.55650851213-36.990097163944.6240423574
20.201513823267-0.006415225806670.1787880390960.8750077360550.344624209510.8529623201730.01564235512730.01887912723590.0242231258144-0.08881223071760.0652235756763-0.120238295506-0.03785402807460.168783026801-0.06901481571440.497370924861-0.0400460862897-0.01352604478750.330107583309-0.001867420217070.29169836957-2.15741205254-20.270609135264.9407521314
30.489517920544-0.02410688282010.08761147102971.022218388830.2875163701981.00225669295-0.0116585538873-0.109806628629-0.03557394440070.3520881080830.0358447425780.03050976665570.0781225561336-0.0685509086551-0.01330284121630.630493678568-0.0371210144238-0.0244512218140.3047209999370.02440105253250.256042593664-18.5573959654-13.098856616397.9562317989
40.5893764678560.648118335273-0.2267191038462.25850599593-0.2017331438460.5062711732340.00817341963327-0.002862745502010.0874760416970.1187669333830.04657100213980.371046641202-0.115096497454-0.182095182545-0.04147419694910.542083254720.0421225428308-0.03405608154930.3685622392780.002275612810090.340741791245-7.2563468545123.7714886007143.722284813
50.588079788542-0.07903268184390.119693415251.14486133293-0.1502875078610.825025152790.0413393888893-0.08258597523710.1067606069210.379670079550.05181788211730.155937693528-0.0635053392539-0.194068050095-0.05117070487440.5567235837890.05098332127110.09766989944920.3671430330780.01514841957330.370650766621-9.5150316157344.0002922892137.727550329
61.923227363490.2268046111180.3329256911471.22738364298-0.2978764828630.431408604207-0.00306733572686-0.0727939007481-0.0512695804179-0.00489992054068-0.00214492415151-0.0407833302631-0.0479199036869-0.006165489986820.03561068757220.599863532740.0306681300036-0.04842296306540.319223588393-0.01615527603040.2260120575098.318190674922.8922456077121.103120191
70.4334658802850.09380249574350.01111526298911.0332715723-0.1729430256490.9036367858660.02235653979870.0453921012767-0.0162389653889-0.1286651131710.06243479146160.1992088337340.0566707832478-0.174858061195-0.07292842152140.4235297936830.0239282624126-0.05892155235820.2755902477450.02594315373330.2954651303650.97141799280645.8308920446105.017501892
80.7172525317930.0958898818631-0.02740537455361.96245317913-0.1517207687561.22206885221-0.02944620765530.0593138083403-0.0583901297946-0.2500717700950.00457021565194-0.3072419594680.003497684508290.2230031853580.02206290675710.3853450817910.04986775496120.01887685442960.296334659424-0.01770112035930.24862389877730.3955826650.542239179898.7979750236
91.26242096579-0.3504524356060.07624366431161.54683263075-0.1092452200661.078334808950.003572119023070.2304898184470.0223656602254-0.420373587609-0.0164519420766-0.01871354287280.0135535313707-0.03340578684160.01773172823630.5617886227280.0299516162176-0.02128442341880.297674694595-0.004941973751020.25293928251814.599136137249.864660159288.5154842952
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 360 through 517 )AA360 - 5171 - 158
22chain 'A' and (resid 518 through 964 )AA518 - 964159 - 605
33chain 'A' and (resid 965 through 1420 )AA965 - 1420606 - 1037
44chain 'B' and (resid 360 through 517 )BB360 - 5171 - 158
55chain 'B' and (resid 518 through 667 )BB518 - 667159 - 308
66chain 'B' and (resid 668 through 819 )BB668 - 819309 - 460
77chain 'B' and (resid 820 through 1023 )BB820 - 1023461 - 664
88chain 'B' and (resid 1024 through 1204 )BB1024 - 1204665 - 820
99chain 'B' and (resid 1205 through 1420 )BB1205 - 1420821 - 1036

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