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- PDB-8ezr: Crystal structure of the HipS(Lp)-HipT(Lp) complex from Legionell... -

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Basic information

Entry
Database: PDB / ID: 8ezr
TitleCrystal structure of the HipS(Lp)-HipT(Lp) complex from Legionella pneumophila, native protein
Components
  • HipS(Lp)
  • HipT(Lp)
KeywordsTOXIN / toxin-antitoxin complex / legionella pneumophila / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / National Institute of Allergy and Infectious Diseases / NIAID
Function / homologyHipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / transferase activity / DI(HYDROXYETHYL)ETHER / Toxin HipA / Type II toxin-antitoxin system HipA family toxin
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsStogios, P.J. / Skarina, T. / Michalska, K. / Di Leo, R. / Lin, J. / Ensminger, A. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of the HipS(Lp)-HipT(Lp) complex from Legionella pneumophila, native protein
Authors: Stogios, P.
History
DepositionNov 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HipS(Lp)
B: HipT(Lp)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8394
Polymers47,6972
Non-polymers1422
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-11 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.038, 45.038, 393.970
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
Components on special symmetry positions
IDModelComponents
11B-534-

HOH

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Components

#1: Protein HipS(Lp)


Mass: 11568.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg2369 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A2S6F3Z6
#2: Protein HipT(Lp)


Mass: 36128.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg2370 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A2S6F402
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG 1K, 0.1 M Hepes pH 7.5, cryo paratone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. obs: 29985 / % possible obs: 95.5 % / Redundancy: 14.4 % / Biso Wilson estimate: 42.18 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.024 / Net I/σ(I): 53.2
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 1222 / CC1/2: 0.841 / Rpim(I) all: 0.326 / % possible all: 81.2

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→32.83 Å / SU ML: 0.2276 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8349
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1486 4.99 %RANDOM
Rwork0.2131 28275 --
obs0.2155 29761 95.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.17 Å2
Refinement stepCycle: LAST / Resolution: 1.95→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 8 185 3219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00453094
X-RAY DIFFRACTIONf_angle_d0.7114158
X-RAY DIFFRACTIONf_chiral_restr0.0473460
X-RAY DIFFRACTIONf_plane_restr0.0076524
X-RAY DIFFRACTIONf_dihedral_angle_d18.30091175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.32461130.30862139X-RAY DIFFRACTION81.92
2.02-2.090.35081260.28982393X-RAY DIFFRACTION91.83
2.09-2.170.32361280.25982467X-RAY DIFFRACTION93.72
2.17-2.270.32381310.25012527X-RAY DIFFRACTION94.52
2.27-2.390.30721320.25982489X-RAY DIFFRACTION95
2.39-2.540.33121350.25852555X-RAY DIFFRACTION95.93
2.54-2.730.27261330.25262563X-RAY DIFFRACTION96.22
2.73-3.010.28361410.24982668X-RAY DIFFRACTION98.05
3.01-3.440.25391420.22652693X-RAY DIFFRACTION99.51
3.44-4.340.26481450.18252774X-RAY DIFFRACTION99.9
4.34-32.830.221600.18353007X-RAY DIFFRACTION99.62
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)
14.60677315539-1.93456422637-2.049423891267.649279658571.505255009695.72168926267-0.614147936479-0.8887907713430.5449616289580.9905699107950.2644983199350.401680024799-0.744723970906-0.8399514059930.2965392655990.9440338015240.440679030841-0.009802314507630.6915306059020.01281974075190.38162384650728.827688569251.9770924517193.45613413
21.47265294791-1.154901563820.8503866833047.555395591591.278270355941.09551434269-0.169192171429-0.479541687816-0.1792426682740.333779989397-0.08905578494590.610557565563-0.86945422149-0.4659125017560.2134944250171.103119576590.37259703859-0.1753993621940.625138645999-0.1572127794930.63422063092631.348031303755.2572747425191.294243629
32.812121382470.1865976545672.643205053086.486350835691.834174960213.24248875914-0.240965263705-0.968032014342-0.03965126269520.469752448827-0.09149585320050.781396883086-0.637982257368-0.9941373460860.3064858049520.9733453602240.557946174166-0.03292050751011.01209322484-0.1396080705680.67891687959421.546253374353.7341692063187.724977434
46.449361235130.711677464459-2.08420999274.89099059268-1.129012527850.8420469367580.611109629745-0.9286030483652.711118435030.01258531065130.217293115357-0.00683061674249-1.751355307530.167462259852-0.7794278547381.488241953420.245818625811-0.08187142284640.628276717722-0.2252386208951.1355599248534.336373660565.4431196937189.965299944
50.62413489583-0.723029728548-0.3796281636423.45115668697-0.625197892120.660421418183-0.137693581233-0.1258779155020.3482878150790.3183395820790.3940011258720.0649029439746-0.372547587412-0.2618376393630.1828695130941.245282094420.68402403561-0.3134017750310.554598786057-0.1503756392810.73464850746927.753964426357.3954087668180.966515467
69.60618241147-4.842064986873.749840297038.6683668422-5.718531927145.451439713810.5476047608190.314008317259-0.0833374600994-2.56842882746-0.2168509643360.841161689339-0.0873812803931-1.33397688515-0.3248698465820.7946525531810.2251024899970.01293038447640.710069673928-0.0107645167120.34909627443931.777706234343.9440405789181.333119835
74.121733663181.94894870426-4.20394611685.95705843196-3.199396333484.59452482153-0.03319513411340.705154514921-0.55078660629-0.477762957046-0.15232020437-0.2438092704120.943872694447-0.6516362439520.2967232291060.551869306861-0.0395729455850.01411557787050.52249205327-0.0007280049341760.47790858608134.729244451630.6942540421186.811802217
84.32223352088-4.435691240514.866777153924.55707098957-4.996661473655.479253025650.7935404623751.29374323804-0.174944277041-0.4753509364170.4484601362820.2951861781130.731183397468-1.12587757807-1.364741854850.6221939421850.0732758146911-0.05972712629630.7798123143220.02587200918830.59861292521326.823205884334.68012457191.111024285
98.74921886885.71665229271-4.596218979195.35779107814-5.710956782878.84558336999-0.249315831476-0.06522361528570.1331945381290.129811516120.272631949105-0.392914390344-0.80713013372-0.635601897016-0.06346615713320.5100493543690.228755147384-0.05275657255030.596265320641-0.07806824616650.42489157998433.998417675243.7028894637188.848116709
105.981476036662.0762363137-5.820568083354.68367131877-1.771289910625.67891830817-0.609389220875-1.07209357748-0.1731504924311.110995847210.152702986283-0.3780661316290.2695756537230.5705338986060.4261931943861.017624384640.384353597755-0.109512799150.614633253759-0.06674073715080.49562735656733.667974381149.7896701061193.596287475
116.067546894580.139625384109-0.02482543434525.00412385832.883880098816.231290781630.3129839036090.8320293617710.61865585772-0.3455817769250.261915437425-1.178177114941.04376968090.522188711542-0.5215088242631.554983078230.03898823506650.1517268627661.231179823510.1841310574941.076659079148.507617810230.5849959333176.376541023
123.64659374640.674292265957-0.2981506468419.143508567044.281067421748.56369852934-0.0841067666814-0.265781042229-0.1214544741780.04568889800830.112057018575-0.4296879645390.310805239522-0.242643890147-0.06315195604210.410631771516-0.04238033320990.03418632280330.3064297312560.02071634990240.3994446477449.056643907733.3328201272182.982977191
131.74050871218-0.7152252679150.5286241158291.319586681940.1363055083224.22014743295-0.1403584569740.1067801149510.00277140649759-0.2182718797120.0163503739426-0.0251694144394-0.305733131250.0767516416150.09750016442250.541589365082-0.10137902122-0.006341476532110.191002155214-0.01075739835560.35487159311744.209804720840.282000619163.388716559
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 8 )AA1 - 81 - 8
22chain 'A' and (resid 9 through 18 )AA9 - 189 - 18
33chain 'A' and (resid 19 through 28 )AA19 - 2819 - 28
44chain 'A' and (resid 29 through 33 )AA29 - 3329 - 33
55chain 'A' and (resid 34 through 54 )AA34 - 5434 - 54
66chain 'A' and (resid 55 through 63 )AA55 - 6355 - 63
77chain 'A' and (resid 64 through 73 )AA64 - 7364 - 73
88chain 'A' and (resid 74 through 80 )AA74 - 8074 - 80
99chain 'A' and (resid 81 through 95 )AA81 - 9581 - 95
1010chain 'A' and (resid 96 through 101 )AA96 - 10196 - 101
1111chain 'B' and (resid 1 through 55 )BC1 - 551 - 15
1212chain 'B' and (resid 56 through 93 )BC56 - 9316 - 53
1313chain 'B' and (resid 94 through 312 )BC94 - 31254 - 272

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