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

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Basic information

Entry
Database: PDB / ID: 8ezs
TitleCrystal structure of the HipS(Lp)-HipT(Lp) complex from Legionella pneumophila, Sel-met 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 / Toxin HipA / Type II toxin-antitoxin system HipA family toxin
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.47 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, Sel-met protein
Authors: Stogios, P.J.
History
DepositionNov 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)48,1553
Polymers48,1192
Non-polymers351
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-16 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.854, 44.854, 392.053
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

#1: Protein HipS(Lp)


Mass: 11709.013 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: 36410.148 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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M KCl, 10 mM Tris pH 7, 20% PEG 4K, SeU soak, 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 PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 14111 / % possible obs: 89.1 % / Redundancy: 10.9 % / Biso Wilson estimate: 34.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.029 / Net I/σ(I): 19.5
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 211 / CC1/2: 0.853 / Rpim(I) all: 0.408 / % possible all: 37.4

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.47→30 Å / SU ML: 0.2723 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 1095 5 %RANDOM
Rwork0.2025 20820 --
obs0.2054 12773 80.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.89 Å2
Refinement stepCycle: LAST / Resolution: 2.47→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 0 1 72 3075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283064
X-RAY DIFFRACTIONf_angle_d0.53354124
X-RAY DIFFRACTIONf_chiral_restr0.0414456
X-RAY DIFFRACTIONf_plane_restr0.0033523
X-RAY DIFFRACTIONf_dihedral_angle_d18.58191163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.590.378870.3703158X-RAY DIFFRACTION4.84
2.59-2.720.399840.29611572X-RAY DIFFRACTION48.45
2.72-2.890.31091570.27522934X-RAY DIFFRACTION90.14
2.89-3.110.28461740.24413211X-RAY DIFFRACTION99.82
3.12-3.430.32211690.22753248X-RAY DIFFRACTION99.53
3.43-3.920.27661670.18853222X-RAY DIFFRACTION99.65
3.92-4.940.20011720.16063259X-RAY DIFFRACTION99.74
4.94-300.21351650.17753216X-RAY DIFFRACTION99.44
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)
14.933877179724.79681581491-1.45025468514.82595409312-0.8448932620087.05717124005-0.313513682304-0.5785689404960.8049088903010.830812816350.2052430044770.68793929584-0.13982430953-0.870974501684-0.03036993569230.6898163977490.321909876424-0.06117219551620.352257239618-0.01731874361590.31043707570428.546549398851.936100627192.481558417
21.17956378246-0.09046635681261.41242299222.293200965690.05408429788081.69856880767-0.089920917271-0.3959834939910.01797644938550.4967121141510.007755380434770.644372175485-0.635322739388-0.3792470069450.1554216687780.5444191839240.1101856577360.08511494724830.124601328461-0.1135805874610.45972312930431.785261707655.5588147257190.136163206
34.165015634490.4736028370140.1246094608965.137936170982.107605372270.98671623919-0.335625581567-0.459054182181-0.1536809991250.264479345105-0.08908488831341.16706791217-0.143911294197-0.208162963804-0.1132098453480.7582566674560.463189369691-0.09274015261160.596700945914-0.06431451935720.63734473158321.921393445653.9561823035186.53381161
41.63521441949-0.769649495879-0.4506310826712.03458726736-0.1307590353350.4817708208640.125472958336-0.1469665377180.6873589469770.3639861977210.04329264871130.318202639019-0.576877234929-0.2085966381910.5501718478290.8908288538980.529815716261-0.17204239510.278949328661-0.2064120989850.41933969295829.792751482859.3550328911181.841089337
50.7574849337940.714187119305-0.2503621608524.40032272566-2.439370591244.10286921725-0.02522127445250.127347435118-0.0067453941409-0.4414012573770.0624985458180.1157974557730.0265166844665-0.547198919664-0.05904356148550.256762856390.0900225639719-0.01716875646360.31285948988-0.09170283772030.22262962263632.715659696439.0199811062186.112394414
66.78702781113-3.56323273211-2.459412667785.103955971441.802249225876.94847452852-0.687964976721-0.708060024371-0.3519718009871.546343674850.4444306703110.2150263904850.9190448062840.1201398734020.8243250765050.8425623144880.212013951523-0.1025513629130.246142309544-0.1994907204090.36638015722332.801224089949.5933144524194.336896141
71.964453918580.696791238206-1.197971500757.268723810880.5176119527133.13114293082-0.1558732686871.46870671663-0.189157285508-0.9633421734830.128404482114-0.682932665550.5839816667140.489227720782-0.1134697699040.47891603967-0.08568527414660.03773472750370.717252201236-0.05316119455170.27598506120548.539149185531.2240820714175.030674906
81.329719193990.00554157074284-0.6770239066442.381842487620.8389784107413.63590603522-0.353542335851-0.142438444996-0.126730128213-0.1001100398170.234927795194-0.18141782990.5540275566650.3211216913010.04042359011590.23307573180.001022609229260.02731811251670.120038870648-0.04204938524720.23420075642252.252315134233.9439568935176.972329246
91.27925463148-0.4274245753460.2620309082341.882597926320.1674275913111.36876262716-0.1445786700130.07372435188030.152287296504-0.1672658347730.0252266641690.0965785287592-0.505987770335-0.05555043627690.04171656494840.456128919596-0.0926709247243-0.0477559630277-0.0351997822801-0.02064802475780.20105444146741.603339819744.1517139422162.00326402
102.68750066809-1.333517212361.628175926383.907333770270.2774175667281.768110895220.2215943075050.301419073763-0.118311210437-0.493154346831-0.2285324650610.1041016700240.6506996900130.184363234655-0.1786146291790.4595982334530.008145013983490.1371136805280.04462015228-0.1434204556060.26852430910650.19189069327.7943129189154.65772867
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 54 )AA29 - 5429 - 54
55chain 'A' and (resid 55 through 95 )AA55 - 9555 - 95
66chain 'A' and (resid 96 through 102 )AA96 - 10296 - 102
77chain 'B' and (resid 3 through 61 )BB3 - 611 - 16
88chain 'B' and (resid 62 through 130 )BB62 - 13017 - 85
99chain 'B' and (resid 131 through 285 )BB131 - 28586 - 240
1010chain 'B' and (resid 286 through 312 )BB286 - 312241 - 267

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