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- PDB-8gaj: Crystal Structure of E. coli LptA in complex with Podisus maculiv... -

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Basic information

Entry
Database: PDB / ID: 8gaj
TitleCrystal Structure of E. coli LptA in complex with Podisus maculiventris Thanatin
Components
  • Lipopolysaccharide export system protein LptA
  • Thanatin
KeywordsANTIBIOTIC/LIPID TRANSPORT / LptA / Thanatin / ANTIBIOTIC / ANTIBIOTIC-LIPID TRANSPORT complex
Function / homology
Function and homology information


glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / defense response to fungus / cell outer membrane / lipopolysaccharide binding / outer membrane-bounded periplasmic space / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region
Similarity search - Function
: / Lipopolysaccharide export system protein LptA / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein
Similarity search - Domain/homology
Lipopolysaccharide export system protein LptA / Thanatin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Podisus maculiventris (spined soldier bug)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsHuynh, K. / Kibrom, A. / Donald, B. / Zhou, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J Struct Biol X / Year: 2023
Title: Discovery, characterization, and redesign of potent antimicrobial thanatin orthologs from Chinavia ubica and Murgantia histrionica targeting E. coli LptA.
Authors: Huynh, K. / Kibrom, A. / Donald, B.R. / Zhou, P.
History
DepositionFeb 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide export system protein LptA
B: Thanatin
C: Lipopolysaccharide export system protein LptA
D: Thanatin


Theoretical massNumber of molelcules
Total (without water)33,9564
Polymers33,9564
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, heterodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-27 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.950, 61.830, 150.330
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 Lipopolysaccharide export system protein LptA


Mass: 14536.247 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6D0DFJ5
#2: Protein/peptide Thanatin


Mass: 2441.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podisus maculiventris (spined soldier bug)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55788
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
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: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.025 M Tris pH 8.5, 100 mM NaCl, 0.05 M MES pH 5.8, 35% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.43→47.75 Å / Num. obs: 16463 / % possible obs: 99.9 % / Redundancy: 11.5 % / Biso Wilson estimate: 11.98 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 23.27
Reflection shellResolution: 2.43→2.517 Å / Num. unique obs: 1614 / CC1/2: 0.98 / CC star: 0.995

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→47.75 Å / SU ML: 0.2389 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.8136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2416 810 4.92 %
Rwork0.1937 15651 -
obs0.196 16461 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.68 Å2
Refinement stepCycle: LAST / Resolution: 2.43→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 0 169 2406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372271
X-RAY DIFFRACTIONf_angle_d0.61723070
X-RAY DIFFRACTIONf_chiral_restr0.0509346
X-RAY DIFFRACTIONf_plane_restr0.0045407
X-RAY DIFFRACTIONf_dihedral_angle_d4.4707307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.580.28291340.23942556X-RAY DIFFRACTION99.89
2.58-2.780.30461420.22042541X-RAY DIFFRACTION99.85
2.78-3.060.2451420.21042566X-RAY DIFFRACTION99.96
3.06-3.50.22851270.17872593X-RAY DIFFRACTION100
3.5-4.410.20621310.1672629X-RAY DIFFRACTION99.89
4.41-47.750.22251340.18352766X-RAY DIFFRACTION99.86
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)
10.7147333257420.06627550872670.5127806155350.6015352896771.406463122823.758193191810.0137251516454-0.0770399004760.0695404224557-0.146224807864-0.0250502066780.255729524406-0.206369842084-0.09975232420950.02947163010570.116240038206-0.0819677049743-0.04224125822820.06050786816840.04363685261910.178370623389-12.23136234-25.4766679887-13.0256505236
25.005429388180.03037623928621.844658507614.79893956685-0.8648325563816.54166312214-0.1992450454850.188154205429-0.407343628457-0.630499612540.254891149852-0.01180047408590.460118624222-0.422926344897-0.02689726635870.464867204689-0.1143426776750.06953336700780.321033286046-0.02788528651470.175587331234-16.3638593086-35.1142734482-29.9048509235
30.6335735735580.1420092134740.1128319810110.9259906416270.4044732785051.30379463209-0.0329823581990.097255537833-0.0860686505106-0.17233245923-0.030094680610.0331709282929-0.00586036715886-0.1101344560490.03947400325160.242482407028-0.0765507725645-0.07354079159440.0675292122493-0.02804693607810.0896914275942-9.67285038995-27.0176410968-23.1465208997
40.696872973412-0.0580100074911-0.1252935349722.070049191132.552970028545.65742434153-0.01272137286830.1106567225290.00700571705796-0.2697103511420.0860817260023-0.00111242758122-0.2973770261490.214255135426-0.09512434278550.117578197172-0.0722545253565-0.07695707208670.0939685869974-0.02033013543710.0993145768285-4.73927667985-23.6758590956-17.0283749995
53.432014412532.789293952850.03788138083965.15830298874-0.1071619707250.9290597468310.03825440530650.0560013869254-0.470735706260.0790825225067-0.00696474279975-0.1492839807840.456390222939-0.2286479383580.008102594574840.501343992855-0.0636972284448-0.08217759578190.177929667203-0.06611813117290.250875610272-11.5496536713-37.0697560979-22.372970931
60.6800234718990.0934329298490.5179372100791.124391650890.7227017058460.8556130550880.1211658607770.211484634702-0.266847403346-0.009170682266790.03581685556530.02766839450010.45277215824-0.182239324632-0.077493536740.300040960541-0.0691084128254-0.04669129458970.109816782093-0.04493945114670.0924893237401-5.21446394742-30.681832882-16.5129110601
72.46222974497-0.507196978634-0.9654158104711.589065135260.3801568721412.755238702680.07324406641110.184820350422-0.100173912582-0.1238680597990.00590697693436-0.1257453539830.01070540900560.0425685631667-0.0606150631741-0.0233993060134-0.005695173398470.02997533968190.215908453445-0.04382501363440.122820506952.36166849605-22.3263975415-6.81479421081
83.909922457431.11243398875-0.3533153254222.3750381092-0.08623829101310.47984440534-0.0356359279910.445031250106-0.579611857487-0.2965798831210.0620613151071-0.1497503598620.602766963135-0.1598499888830.01992440962680.4016083459220.0159185928839-0.04646187667450.165049943851-0.08391916812170.178740244805-2.19814806977-35.2220420439-14.1373121833
91.567897994270.637819285673-0.1061521305791.84211859835-0.2397181504530.8747178077560.05676667643340.13657755550.07675775532-0.2059382936-0.24651963757-0.0120812399595-0.0904037719753-0.1697575080010.0600432886182-0.02737783177130.1206743423020.04084879755820.248662645721-0.05902011054230.1474445686566.85204988544-15.1380905863-10.5942746128
101.433255887670.5941993722972.250526067110.5483278997821.115130954353.638785904480.0598096420626-0.3469182307570.1869773892980.302338158060.0717511955956-0.447988857542-0.3460028542660.360341634566-0.1298340344380.190725652433-0.120162489308-0.06584569990670.289837455662-0.05213971980970.21758611915423.5778464189-1.9428812006-3.68242968197
113.747854522394.184935304540.6826727682335.957897534481.815980076322.271060582820.489067024144-0.887361358802-0.6722318578130.707135634733-0.475978393628-0.7319686902680.4026630486970.00297404880661-0.02385230689090.357508792311-0.259040562138-0.1214442387090.375270669020.1262206852170.355001799077-17.3105896514-33.4816161264-10.9823968883
121.860123616920.333204877550.668380742282.011424203080.3752096250380.7011826152990.0693126995472-0.0784714871121-0.21326537068-0.07594342556620.08499419946320.1038458560580.319789164951-0.206242888394-0.06378910388380.23813483505-0.146467007815-0.02983775329890.166960232178-0.008290047506120.278349292508-18.9344162137-24.0454944872-24.7692730784
130.896732238412-0.6572288692620.4876718471810.957225781439-1.170024527931.650244717360.11454892182-0.0516745986817-0.0868645709493-0.1116694069790.0193538928594-0.01070193088480.03377071285480.176405513419-0.0752589961401-0.00546218598391-0.0436000520476-0.01423001351270.119356506522-0.03163816527480.13240897624923.4071993215-11.3295107852-23.0252704168
144.17730499597-2.123014632031.133566060451.09303694425-0.2642329120827.23342702698-0.09606675091340.3255761557810.468600266416-0.516256830402-0.00758396029541-0.070657374126-0.5380567386930.2969547650790.1033069747660.3644489647590.0978858803645-0.07190660919230.2464245766590.02865213941260.2429395182418.5978580835-0.978053318422-39.9432262835
150.848680242958-0.307514718490.6118729840990.795109228788-0.6622536306840.891453529177-0.00139510031930.208814366380.0964881982224-0.212836211697-0.05389340757580.115254900705-0.01548932356080.0950218091842-0.00229311341780.1878602261130.0743738910207-0.1410558985210.05976367194990.008684765989750.019222084644215.8731915682-9.16253688016-30.3769295602
165.15861414457-1.018824147143.770660838721.2114949512-1.122334149814.806939577630.1543671751440.116577689827-0.0953323191966-0.264983625053-0.01647824090570.2292972355250.0906983198291-0.266400945489-0.1889767947380.08055877262660.0412913607205-0.09370358331170.07762626464970.03272061565410.028377288488114.6608008495-12.3192350351-22.5002997986
171.88409815139-0.05543050491040.1599853836452.391299814-1.260510063662.29857679611-0.05524287372240.2145287985320.392766781362-0.259429047363-0.060420731895-0.173928106265-0.5344662630610.1836046686230.3263009821590.5559406629610.0391447164877-0.04790920457180.07394327467720.1139932161160.13745335856219.83653284110.500789773643-28.3002223147
181.637520603790.545164839261-0.06785509333181.77656817346-0.4472652550661.156624292990.02424188772160.2054109358810.167121676647-0.194094997611-0.00809601521660.30003209844-0.0752773696033-0.192429855845-0.0680122130455-0.01063168945270.150330904624-0.1216663905530.1238553714650.01278214209650.060895257328411.2017029488-11.6561646635-18.4288725447
191.83902769385-0.1437963924790.5420948623291.12617069329-0.5162370390521.57342106546-0.002388564245870.2173260187170.15733469449-0.237178632171-0.002814237361280.218890614869-0.284230622117-0.123691085262-0.05713306280340.05882564380380.0844445689606-0.07372225502060.155124146770.04888850425860.097396134648613.6894858071-8.51310525089-14.6508336022
200.6862581585350.3409350661030.1489938403330.504106058932-0.1715708392460.224755306428-0.01724355447450.0100842477524-0.0469825859292-0.15913261495-0.128579196506-0.0428394485869-0.112422402493-0.02351368130930.008379434357890.09288688601430.190905591325-0.09421405047920.2020629702450.0001007233326550.17591808243711.2784857008-13.4044812224-13.1110364005
211.42915743931-0.0367567195463-1.45669776850.617251667548-0.7259027808352.43459197513-0.173427125069-0.13455258004-0.2445008529950.0808557684375-0.1128730763680.2721222690260.5026486927-0.2396669343510.2503404270160.189579330368-0.1208139978030.003804434530230.26359573564-0.02349978761620.237809732468-7.30932008693-31.32062807461.48587979382
226.190651498453.22837136182-3.059465867735.70138009276-3.475429032962.447750089220.40586364178-0.6184973546750.2732502077790.697955125454-0.3592502472350.01845917535-0.4499011181630.323058522329-0.07555194638360.437560584088-0.2903510258670.1123800550170.326832959240.008629308706810.30653911744129.7134303625-4.22392724849-24.0617904217
233.74875963681-0.119081759433-1.743021594360.5065535173880.007160927351413.68592186962-0.2712112959120.8195079529730.0745339373984-0.8184063555260.189080443891-0.0189761373789-0.4389550608140.3867763412970.06491259464720.629685076556-0.07981503902970.04763423557250.3656157272250.003403111321870.17138524206122.3583846739-13.1599636733-36.4569801102
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 41 )AA28 - 411 - 14
22chain 'A' and (resid 42 through 50 )AA42 - 5015 - 23
33chain 'A' and (resid 51 through 62 )AA51 - 6224 - 35
44chain 'A' and (resid 63 through 70 )AA63 - 7036 - 43
55chain 'A' and (resid 71 through 79 )AA71 - 7944 - 52
66chain 'A' and (resid 80 through 98 )AA80 - 9853 - 71
77chain 'A' and (resid 99 through 109 )AA99 - 10972 - 82
88chain 'A' and (resid 110 through 124 )AA110 - 12483 - 97
99chain 'A' and (resid 125 through 141 )AA125 - 14198 - 114
1010chain 'A' and (resid 142 through 154 )AA142 - 154115 - 127
1111chain 'B' and (resid 3 through 8 )BB3 - 81 - 6
1212chain 'B' and (resid 9 through 21 )BB9 - 217 - 19
1313chain 'C' and (resid 28 through 41 )CC28 - 411 - 14
1414chain 'C' and (resid 42 through 50 )CC42 - 5015 - 23
1515chain 'C' and (resid 51 through 62 )CC51 - 6224 - 35
1616chain 'C' and (resid 63 through 70 )CC63 - 7036 - 43
1717chain 'C' and (resid 71 through 89 )CC71 - 8944 - 62
1818chain 'C' and (resid 90 through 98 )CC90 - 9863 - 71
1919chain 'C' and (resid 99 through 115 )CC99 - 11572 - 88
2020chain 'C' and (resid 116 through 141 )CC116 - 14189 - 114
2121chain 'C' and (resid 142 through 154 )CC142 - 154115 - 127
2222chain 'D' and (resid 3 through 8 )DD3 - 81 - 6
2323chain 'D' and (resid 9 through 21 )DD9 - 217 - 19

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