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- PDB-8qjc: T6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core doma... -

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Basic information

Entry
Database: PDB / ID: 8qjc
TitleT6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core domain with toxin domain
ComponentsT6SS-associated Rhs core and toxin domain
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 / MOLECULAR REPLACEMENT / Resolution: 2.491 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 / _citation_author.identifier_ORCID
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: T6SS-associated Rhs core and toxin domain


Theoretical massNumber of molelcules
Total (without water)173,1541
Polymers173,1541
Non-polymers00
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area47830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.443, 118.326, 169.755
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

#1: Protein T6SS-associated Rhs core and toxin domain


Mass: 173154.047 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 ul of protein solution (2.29 g/l) was mixed with 1 ul reservoir solution (0.1 M MES pH 7, 2% ethylene glycol, 7% PEG 8,000). A crystal was flash frozen without additional cryoprotectant.

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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: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.491→49.62 Å / Num. obs: 50747 / % possible obs: 99.09 % / Redundancy: 24.59 % / Biso Wilson estimate: 32.35 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.2273 / Rpim(I) all: 0.04691 / Rrim(I) all: 0.2323 / Net I/σ(I): 17
Reflection shellResolution: 2.491→2.58 Å / Rmerge(I) obs: 1.079 / Num. unique obs: 4813 / CC1/2: 0.826 / Rpim(I) all: 0.2233 / Rrim(I) all: 1.103 / % possible all: 95.18

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.20.1_4487refinement
Coot0.9.3model building
BUSTERrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.491→49.62 Å / SU ML: 0.2899 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 23.2137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2277 4758 4.99 %
Rwork0.1902 90669 -
obs0.1921 50701 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.41 Å2
Refinement stepCycle: LAST / Resolution: 2.491→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8535 0 0 555 9090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00268741
X-RAY DIFFRACTIONf_angle_d0.515911871
X-RAY DIFFRACTIONf_chiral_restr0.04241233
X-RAY DIFFRACTIONf_plane_restr0.00461577
X-RAY DIFFRACTIONf_dihedral_angle_d13.81033220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.491-2.520.37871430.29132624X-RAY DIFFRACTION83.75
2.52-2.550.30151620.26333050X-RAY DIFFRACTION98.74
2.55-2.580.27231570.25073007X-RAY DIFFRACTION98.81
2.58-2.610.31461640.24273054X-RAY DIFFRACTION99.6
2.61-2.650.31361630.23433077X-RAY DIFFRACTION99.42
2.65-2.680.29891570.2353036X-RAY DIFFRACTION99.13
2.68-2.720.30981580.23993037X-RAY DIFFRACTION98.95
2.72-2.760.25491590.24113060X-RAY DIFFRACTION98.14
2.76-2.810.30671600.25352953X-RAY DIFFRACTION97.99
2.81-2.850.31321600.23523090X-RAY DIFFRACTION98.37
2.85-2.90.2621520.21682961X-RAY DIFFRACTION98.67
2.9-2.950.27121610.20943098X-RAY DIFFRACTION98.94
2.95-3.010.28741570.20793072X-RAY DIFFRACTION99.38
3.01-3.070.25641610.20343065X-RAY DIFFRACTION99.29
3.07-3.140.25351610.21173051X-RAY DIFFRACTION99.11
3.14-3.210.26051590.21373043X-RAY DIFFRACTION98.92
3.21-3.290.26931620.21763057X-RAY DIFFRACTION99.08
3.29-3.380.24381590.19733058X-RAY DIFFRACTION99.14
3.38-3.480.19971560.17852994X-RAY DIFFRACTION97.89
3.48-3.590.21521580.17063080X-RAY DIFFRACTION99.23
3.59-3.720.19211600.16382986X-RAY DIFFRACTION98.22
3.72-3.870.23671610.17063063X-RAY DIFFRACTION99.44
3.87-4.050.19431590.16773071X-RAY DIFFRACTION99.14
4.05-4.260.15961580.15493048X-RAY DIFFRACTION98.74
4.26-4.530.16181650.13673042X-RAY DIFFRACTION99.2
4.53-4.870.17561560.13542984X-RAY DIFFRACTION97.42
4.88-5.360.18141600.16163010X-RAY DIFFRACTION97.42
5.37-6.140.19241550.18753016X-RAY DIFFRACTION97.57
6.14-7.730.24381530.19722985X-RAY DIFFRACTION97.09
7.73-49.620.19371620.19212997X-RAY DIFFRACTION97.44
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)
10.2654982896970.2950716322120.1866696037841.14472981951-0.2822651263420.4212073215960.04425021157330.009008567067650.1085214078980.382995669791-0.04277310753420.252451415425-0.0372996013965-0.0343133379704-0.06074582870830.310145872715-0.004046866382030.02303121634540.2619881810810.000214379515010.2956552335686.0279458212811.4525533105-17.1208571671
21.47851123845-0.458102630856-0.610884040280.3288168360350.4747356741230.790718425273-0.118246104035-0.1831944772970.1549071849460.1916321050.1308317738730.00171670719726-0.0313258380564-0.07359559551540.05868062406330.3085875372310.0318201991827-0.01065668510320.2876895506030.001308864103260.2338387342052.82318616815-5.1936236212-10.2203656934
30.681319384174-0.0320346348042-0.03552215664320.6721064645820.09265911229310.3478346692230.00332720031543-0.1102036185480.003618802138610.0498170487749-0.00657696816996-0.013212682653-0.0656614412352-0.04044149738480.006643791714080.2455962144850.00320689895788-0.04745397813670.2192219960390.03119316598140.141316563073-3.5207609767211.6461146242-19.822783578
40.351277870446-0.287630722948-0.2829816806391.01935077099-0.02480316974560.3990144389130.0708428592262-0.01763791972440.0622341306557-0.124174718875-0.0520950022582-0.123177686492-0.0604502151977-0.0174131192451-0.06134646519760.271032781514-0.00413675312585-0.04132933511110.308040364370.00552062258940.2759843313460.2588339718923.72762384899-48.3400749291
50.4488877662270.006319508658780.1832118848860.4573697974930.09933945245680.273379796855-0.00468448215433-0.0255788215581-0.02054912809230.03622391361040.01187586638040.09109924963810.0274035456104-0.05458217409880.003631993454050.2067074865820.003091449434620.002843431933320.1875477298180.01906908571510.174310521448-24.668547373720.4369491174-43.812057263
60.5561955212071.119610470860.7412915474432.606971742881.636107590271.10855134730.01830807954610.153267801567-0.0149873173187-0.3741447025370.0570084775194-0.0536011582226-0.1442373455450.1258388443560.01793873983980.2557963982830.02947618086640.002391390776960.246541747116-0.006666389000520.193089711945-16.318961180720.9786520637-74.6928052027
71.98144656133-0.108574119393-0.6072727422831.15007925925-0.08134754910971.17683349391-0.01667846746870.2645873090390.0921486903058-0.1933482127490.05677456824070.197969754181-0.103147430274-0.226732735611-0.05025132405810.2781672292650.00625942946165-0.04288644023280.2290063696960.01839314027360.269745064534-25.25860579345.4648642142-64.1129938831
80.306086581676-0.00623005952277-0.08817688300331.73628602760.6197132488421.119296766280.01011357182270.04803374091420.0143593366287-0.103079108243-0.04154668722620.152711420089-0.0709472441976-0.08958033064920.02047828315150.1912159700150.0083735543047-0.02188620783650.249064895030.01446534081890.246121417085-34.674408130124.9211602424-58.8250893463
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 360 through 415 )360 - 4151 - 56
22chain 'A' and (resid 416 through 487 )416 - 48757 - 128
33chain 'A' and (resid 488 through 730 )488 - 730129 - 371
44chain 'A' and (resid 731 through 819 )731 - 819372 - 460
55chain 'A' and (resid 820 through 1065 )820 - 1065461 - 706
66chain 'A' and (resid 1066 through 1132 )1066 - 1132707 - 773
77chain 'A' and (resid 1133 through 1229 )1133 - 1229774 - 857
88chain 'A' and (resid 1230 through 1420 )1230 - 1420858 - 1048

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