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- PDB-9oij: Structure of S. Typhimurium 14028 Gifsy-1 prophage HepS -

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Basic information

Entry
Database: PDB / ID: 9oij
TitleStructure of S. Typhimurium 14028 Gifsy-1 prophage HepS
ComponentsHepS
KeywordsANTIVIRAL PROTEIN / HEPN / tetramer / tRNase
Function / homologymembrane / Prophage protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSargen, M.R. / Antine, S.P. / Grabe, G.J. / Antonellis, G. / Ragucci, A.E. / Kranzusch, P.J. / Helaine, S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: Nature / Year: 2026
Title: A prophage-encoded abortive infection protein preserves host and prophage spread
Authors: Sargen, M.R.
History
DepositionMay 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HepS
B: HepS


Theoretical massNumber of molelcules
Total (without water)47,8712
Polymers47,8712
Non-polymers00
Water1,36976
1
A: HepS
B: HepS

A: HepS
B: HepS


Theoretical massNumber of molelcules
Total (without water)95,7434
Polymers95,7434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6980 Å2
ΔGint-47 kcal/mol
Surface area36310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.717, 130.717, 44.797
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21B-301-

HOH

31B-338-

HOH

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Components

#1: Protein HepS


Mass: 23935.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal GS linker
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 (bacteria)
Gene: STM14_3211 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): LOBSTR- -RIL / References: UniProt: A0A0F6B549
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M CaCl2, 0.1 M Tris pH 8.5, 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.028→32.69 Å / Num. obs: 27169 / % possible obs: 100 % / Redundancy: 20.7 % / Biso Wilson estimate: 49.62 Å2 / Rpim(I) all: 0.032 / Net I/σ(I): 12.2
Reflection shellResolution: 2.028→2.063 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 27169 / CC1/2: 0.423 / Rpim(I) all: 1.667

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSJun 30, 2023 (BUILT 20230630)data reduction
autoPROC1.0.5 (20211020)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→31.39 Å / SU ML: 0.3774 / Cross valid method: FREE R-VALUE / σ(F): 8.55 / Phase error: 38.5377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2968 1290 4.75 %
Rwork0.2465 25879 -
obs0.2491 27169 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.85 Å2
Refinement stepCycle: LAST / Resolution: 2.05→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 0 76 3074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023052
X-RAY DIFFRACTIONf_angle_d0.46054125
X-RAY DIFFRACTIONf_chiral_restr0.0378482
X-RAY DIFFRACTIONf_plane_restr0.0038523
X-RAY DIFFRACTIONf_dihedral_angle_d11.13651146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.140.46511220.38882453X-RAY DIFFRACTION84.37
2.14-2.230.38141390.34522904X-RAY DIFFRACTION99.51
2.23-2.350.35051570.30492867X-RAY DIFFRACTION99.87
2.35-2.50.29081300.27162922X-RAY DIFFRACTION99.97
2.5-2.690.34241470.26982882X-RAY DIFFRACTION99.93
2.69-2.960.30881510.29222930X-RAY DIFFRACTION100
2.96-3.390.35281430.28062933X-RAY DIFFRACTION99.94
3.39-4.260.27311330.22932964X-RAY DIFFRACTION100
4.27-31.390.26191680.20553024X-RAY DIFFRACTION99.94
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)
16.254917500165.351011635143.17962713974.78506651812.69527889411.64763249738-0.176882961782-1.35383793609-0.7967811730041.745903263290.180897091548-0.2263678445790.9769431699990.960690923559-0.175148682460.7436610050560.06903664776330.00967670231410.764087936256-0.0980873603330.77280503893460.9189637837-23.07297932971.34022992357
23.581172365311.070624050710.780047922593.767492018211.875490798023.535074999860.01066293267880.1602133675470.04620087052610.098122032614-0.162974228642-0.1427928472810.365974572345-0.1129315994150.2361390687280.4536070208650.002718106415860.0516498738480.4492303068950.01340056364790.53724503135552.0122586341-19.8597333479-2.19388970025
36.91183433851.709220015251.394267064715.499369604432.76910757694.769873844720.03439635856970.1871477444191.366051658820.62899264785-0.2822722598280.2022390368540.213871935878-0.0992574777470.2231705392430.554920796440.00486625526567-0.006172632397940.5656077414290.05552066380920.78162046196655.8827721389-5.5711573261913.8133353552
43.511271381471.13993040738-0.108612924153.125127415031.363252647553.51638762723-0.1051594473760.5427105207020.50597428912-0.355819144052-0.07300543883930.294573685655-0.102416625217-0.3944091970640.1675468989290.4904992346650.0203498315194-0.009672034051540.4757768462070.1308370691540.58724033135956.337197022-10.4898628724-9.25588312279
51.855590281691.726770905060.5860958405945.283020905062.412905510132.55040109086-1.44074552038-0.837292358402-2.003317691750.03209968068751.429282598270.2054031774460.562346688195-0.2021070651820.2352456830710.8818539788880.01229079784270.1772245884511.115045194150.1917344919591.3981697516650.4792415563-32.0409487433-17.6154170425
69.39853543163-0.1768175084941.785919758952.7968122263-0.04638139707993.02690097381-0.6822348608850.3873326042820.546232944779-0.3073895498820.277332293404-0.206289976462-0.5108677472040.3227092599040.2778187277260.3633245545250.0151762277330.06670237933560.2611092756620.007613630154190.43992780012161.3341041935-16.4369703954-6.11223279357
75.88645212836-3.20811492717-1.123024453718.65275192267-3.841587276883.00197735330.4090719216610.4140500928890.14219712867-1.03847326623-1.038452903612.02558843667-0.633891217954-0.5954742282720.5131091371390.901648172150.065141949628-0.2712515954490.74334839866-0.008492084188850.89775172083974.2495598514-28.22861086254.88907120091
87.69935834764-5.08816925763-2.20454031085.727058120163.859538065073.998367619811.601099421673.208302016650.346509069442-3.46976542055-1.42492076649-0.0488754010161-1.26336878719-0.292121554456-0.03134524764020.9915092229590.0748662143667-0.002536198876190.86610241614-0.004892042779330.75651122615923.2738917745-16.8109787298-8.11431679501
96.51631252408-3.459546870240.2817654007067.56259773852-0.5353251169022.71914668477-0.06920634021360.401590199077-0.128954241056-0.614361077456-0.0470754294337-0.2837583782240.237732501766-0.07171778482320.06363829735120.376454215939-0.1220859996660.06011807734840.467742625636-0.05901817718580.37709461932232.0832775428-19.7424661583-3.59382416612
105.31780052577-2.04788574101-1.951103774158.655963318580.5452503427274.500158330280.1016645342460.158342026186-0.013620514328-0.0983580889604-0.41554696568-0.030665019483-0.07048180231730.2566446514130.2739471483550.358138985749-0.0376715793696-0.0423918048970.50416555348-0.08730611880270.63721119835529.4581310738-2.146747344652.5609076009
114.69700132656-1.04731080711-1.019178936212.43532493871-0.1053752962213.01193428463-0.0295849403713-0.7195443610020.1036927518450.2337605793450.0162654000955-0.1650676987950.5102059893320.2329026327480.02260189807890.584565030574-0.06463677545470.06070941207680.534213971743-0.001391079182580.63265463030536.0985589815-22.39243031859.74065801493
126.50321081066-4.854554774590.5796900250788.20478639178-2.799223734172.528401757540.3464036990640.0687399728214-1.16447497043-0.370303905287-0.6453841941011.295838553490.609551118614-0.4093085036810.3365215783710.712422836851-0.1750798426370.06721559334590.711740799321-0.125201940571.1193279095619.400017696-27.65677989444.33175767701
135.92578731719-4.19366394449-0.6553210953737.225736578941.275436832152.579980109530.0558757591899-0.0325187480417-0.3825450820550.111275284811-0.3343781072660.7516081227060.325718640134-0.2530877269760.381678412420.446493753949-0.1598271598190.06776273102670.480451264396-0.06044302775380.56800253458824.4807708772-21.43517806371.95798360049
144.190737536384.474374272283.733760925384.900957751044.461639762528.497231874920.3332059882360.946201526168-0.9528625998021.13351568332-0.9475583583461.728002984110.584158060253-0.1142913104110.6761020996940.823205260282-0.0135903084429-0.04269667532991.04394576112-0.3325009298772.0369054374910.5186506685-6.94342980472-8.20425912641
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 17 through 23 )AA17 - 231 - 7
22chain 'A' and (resid 24 through 58 )AA24 - 588 - 42
33chain 'A' and (resid 59 through 72 )AA59 - 7243 - 56
44chain 'A' and (resid 73 through 152 )AA73 - 15257 - 136
55chain 'A' and (resid 153 through 167 )AA153 - 167137 - 151
66chain 'A' and (resid 168 through 194 )AA168 - 194152 - 178
77chain 'A' and (resid 195 through 207 )AA195 - 207179 - 191
88chain 'B' and (resid 16 through 23 )BB16 - 231 - 8
99chain 'B' and (resid 24 through 58 )BB24 - 589 - 43
1010chain 'B' and (resid 59 through 86 )BB59 - 8644 - 71
1111chain 'B' and (resid 87 through 125 )BB87 - 12572 - 110
1212chain 'B' and (resid 126 through 164 )BB126 - 164111 - 149
1313chain 'B' and (resid 165 through 195 )BB165 - 195150 - 180
1414chain 'B' and (resid 196 through 201 )BB196 - 201181 - 186

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