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- PDB-8gak: Crystal Structure of E. coli LptA in complex with Chinavia Ubica ... -

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Basic information

Entry
Database: PDB / ID: 8gak
TitleCrystal Structure of E. coli LptA in complex with Chinavia Ubica Thanatin
Components
  • Lipopolysaccharide export system protein LptA
  • Thanatin
KeywordsANTIBIOTIC/LIPID TRANSPORT / LptA / Thanatin / ANTIBIOTIC / ANTIBIOTIC-LIPID TRANSPORT complex
Function / homology: / Lipopolysaccharide export system protein LptA / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / lipopolysaccharide binding / periplasmic space / Lipopolysaccharide export system protein LptA
Function and homology information
Biological speciesEscherichia coli (E. coli)
Chinavia ubica (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)33,3684
Polymers33,3684
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The complex remains dominantly as an single heterodimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-23 kcal/mol
Surface area15690 Å2
MethodPISA
2
A: Lipopolysaccharide export system protein LptA
B: Thanatin


Theoretical massNumber of molelcules
Total (without water)16,6842
Polymers16,6842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-5 kcal/mol
Surface area9770 Å2
MethodPISA
3
C: Lipopolysaccharide export system protein LptA
D: Thanatin


Theoretical massNumber of molelcules
Total (without water)16,6842
Polymers16,6842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-4 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.510, 62.130, 150.080
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: 2147.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chinavia ubica (insect) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.28 Å3/Da / Density % sol: 62.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.025 M Tris pH 8.5, 100 mM NaCl, 0.05 M MES pH 5.8, 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→47.86 Å / Num. obs: 34382 / % possible obs: 99.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 37.73 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 20
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 3364 / CC1/2: 0.974 / CC star: 0.993

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.86 Å / SU ML: 0.2187 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.6692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2395 1710 4.99 %
Rwork0.1975 32564 -
obs0.1996 34274 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 0 139 2356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692281
X-RAY DIFFRACTIONf_angle_d0.89243092
X-RAY DIFFRACTIONf_chiral_restr0.0679355
X-RAY DIFFRACTIONf_plane_restr0.0066414
X-RAY DIFFRACTIONf_dihedral_angle_d5.247317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.33971380.30822629X-RAY DIFFRACTION99.28
1.96-2.020.28171410.24142643X-RAY DIFFRACTION98.86
2.02-2.090.26641380.22122667X-RAY DIFFRACTION99.01
2.09-2.170.24591390.21072675X-RAY DIFFRACTION99.43
2.17-2.270.24631430.21332695X-RAY DIFFRACTION99.54
2.27-2.390.24641420.2032684X-RAY DIFFRACTION99.68
2.39-2.540.32471410.23612695X-RAY DIFFRACTION99.93
2.54-2.740.27731410.21182705X-RAY DIFFRACTION99.86
2.74-3.020.25131440.21172728X-RAY DIFFRACTION100
3.02-3.450.24131440.19722754X-RAY DIFFRACTION99.9
3.45-4.350.18861450.17392762X-RAY DIFFRACTION99.97
4.35-47.860.23581540.1852927X-RAY DIFFRACTION99.84
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)
13.83123196710.5132759269811.953290106142.473860614361.466380948067.637840178930.100566140027-0.124643187017-0.1499648273730.3089513489150.0128519253463-0.1139981176730.133062472997-0.180839234755-0.08886150107550.2718939812170.0004824241800080.01081302928410.2975701052110.01210188524260.322122331565-21.407706376220.599986739227.2166874047
23.833592650350.1096133165421.538549572676.001666879232.150195765579.78821861673-0.0465515598497-0.2495936492350.269029576190.53957545645-0.002767264595330.10246700048-0.583031699371-0.2729402484920.03682721180980.351740541261-0.05832445308130.007668454440830.2751061308240.04713798973390.264598822218-17.506276732624.658436159632.6280193709
32.236099021493.715851334451.81531379349.255853300284.511986111542.308064954260.742470910781-0.324125489391-0.9109583908230.498005966442-0.0373446176726-0.5847287420320.9161348180930.632763062384-0.4846027144990.335947693418-0.0288482241881-0.007729843673640.3693613713210.003274900476340.31774503106-14.526363112218.122685168822.445103194
47.87366959291-3.0332994857-0.9974288147266.354061391251.286423975398.575040587910.2289556381930.3640551681480.5334878418760.0194906199085-0.3024824098610.177050615923-2.01773551061-0.7654971931010.1584712063310.7148870996260.0124896998352-0.07807692510250.288777714873-0.03713534848850.330407049476-19.547770230830.664423988428.473769946
55.019779334221.429763172220.3276113804234.412204309721.348866963693.375156401950.06032335862330.195181676982-0.2249173974090.194678350472-0.040076685053-0.266162177283-0.1892391853620.592779039941-0.02757827621720.257188233805-0.0440268754527-0.0236306472750.3809512129490.01102313081820.325232052516-11.912417564318.351039528314.2097748106
63.097005371271.18842614985-0.7105356053492.589295878410.6454949013837.15957501260.2839743877450.7976359054170.746583023215-0.0451692423285-0.384690767394-0.332804849908-1.620960842810.3836182507890.09542093685060.724941976732-0.0892379450343-0.07576985971690.3451006507990.04671083743250.413974139027-16.561347856830.19038538420.6694864289
72.49277910535-1.805827183460.266198102164.611067805750.104960074552.853037751670.1172958332270.0374576815203-0.04752756672290.243003558479-0.1262992093670.146770101188-0.1151009933670.120925750146-0.01621755357980.277641028224-0.169678452452-0.01078541708350.4641857305290.01853662771150.328420238341-9.5681906446816.189009125812.7871218274
87.126997726153.44596474965-4.049456092773.96937028827-3.920899104155.483170716670.652121587164-0.605021859646-0.0803161633954-0.281632952193-0.5921577080720.1870148401310.07752489518160.6406020777350.006082237067870.4976685567710.0315184461221-0.06444039023490.458474467016-0.03631300321640.3761139647867.87945227228-0.365326598888-1.38191412155
92.733356403093.235920256743.835833082524.611627919425.209513308155.960744799730.03210196357030.07030247628061.15859553972-0.537015943175-0.4407472712810.498613726697-2.3133087176-1.713977920970.07418767662270.6108652077550.255433735020.0325143414290.6664733280570.009151352099760.475365752269-29.183563438126.546815463723.103827141
108.96834186679-3.058946195623.457798444463.26046575471-3.92531782774.97015686788-0.388948184981-0.344707129776-0.4780358202921.158775200940.307569078930.186008790238-0.0360128891708-1.079916660550.1031523377710.5668059329750.03225922811330.03089654925550.5072960892990.006606109151110.321608604155-23.301177522516.697841183935.2491026971
115.9968333573-3.094777778626.970782506261.79421457577-3.725019672778.141050700560.3490607236960.1096993658560.410571402182-0.155255954271-0.12889215995-0.07899544281170.04567413415580.168854344312-0.07270125278190.3116320564830.03252241188950.05851758091890.529576372548-0.0473813305660.40740312022712.79576059213.709506427025.05808969625
122.81881471169-1.762734459570.7499837981885.529456176761.949304415242.194855345240.0281554021183-0.05833107513980.2948392903670.405907658553-0.0871178232604-0.129228300092-0.6693126199870.124818146383-0.0007995634618670.3119077716230.003096699704330.007840540948790.3991493673040.01071173029910.37698787523514.51045818694.6029351716325.1008154299
136.378565825460.3807645366340.1080718710722.56210327684-2.013572684067.244594259390.141642123796-0.322029812631-0.682326401348-0.218710513040.27732076079-0.3173377414861.047828374230.496674323049-0.383589265960.3987142783140.0319978517776-0.07570005190780.286931217594-0.02279913533770.32427070173813.1831407443-0.76567272416324.9343895553
144.341851110945.74228399698-5.05641173469.21649437745-7.109391406575.966602389760.19419032692-0.5031638756710.5169339383750.5339281496190.07919785956590.356989225117-1.02261573122-0.211380224631-0.3324320589290.2836067835920.0130419813193-0.02142580470650.4069951791670.001252020942560.3601620806785.783782288376.9106854770816.9263191114
158.75602108093-1.87261440281-1.990305545336.908558986932.467938522132.811535914050.156508925703-0.310400829239-1.013732311480.3476833805680.132140020971-0.4070415540291.238226965240.118038434949-0.2079561770970.5733861032640.0242521357505-0.1339698884140.3038032092370.03633563607370.50895576337911.9260278401-6.7002402126319.2788692036
163.73826463943-0.863862216514-0.4021997074661.37906091254-1.814772829029.422948182790.02781586106030.155461595461-0.12518014339-0.02692040962190.003924761889710.0602110339990.243981488554-0.790755191166-0.1200113135420.266454635595-0.03287774341410.004163541284460.438604478524-0.006380166272550.380411921308-0.5522176086227.4427052164111.0941037123
174.26566840476-2.33849192999-4.184798986557.799478055822.524221268494.105698148260.3783020086070.49897926602-0.894198786605-0.264355467073-0.3042872942770.05736482133881.12966308503-0.6155322689750.008971105098450.644042808652-0.0756939596534-0.08488555288890.467914992146-0.02503622616530.4691823399815.36255975981-5.2061618911314.3150343329
182.39106626588-2.584698607820.08796753116487.81052909897-0.6950460321142.393607656030.2241130551570.100095307342-0.0313663043318-0.136516187409-0.242960492244-0.09882211168060.1306764759450.00530960615538-0.04091064632120.260178505807-0.1780254957-0.01954670481620.5375800518760.01697296064680.343949685538-3.929224902969.7742976836611.2428838968
195.05201621115-5.86890138736.417849209027.23164520339-6.680234899518.188252456680.8431985479560.665221210462-0.159786719201-0.190322256775-0.3928162728860.817516264089-0.132909189312-0.0297282900516-0.3710945500390.4691741859830.1463371570620.02027953819880.60893766770.02127162909110.450471702835-23.474823580729.41358165323.12484764397
206.196926222323.36648252835-2.697492427947.991436896955.046258250868.101710271940.548418406670.848161695956-1.70519601822-1.65571779148-0.0589546173832-0.905025764054-0.04291456579120.442182764747-0.4816574900780.6907983207070.331633312718-0.02327643273720.517234601108-0.1529289585090.51554087051517.7283501048-2.966533472129.87424896971
215.841037292860.5163961156790.7115930766249.14740089494.100177190575.864536620440.3448742539780.4667323084690.1672761528320.246275821003-0.150074769318-0.9408255333680.452397435470.586023353535-0.1504472656910.3563613315470.0409823892085-0.03051904008610.3854982850460.01954983445430.38904699581819.94360814126.6646020197723.8917785005
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 28 through 46 )CC28 - 461 - 19
22chain 'C' and (resid 47 through 62 )CC47 - 6220 - 35
33chain 'C' and (resid 63 through 70 )CC63 - 7036 - 43
44chain 'C' and (resid 71 through 89 )CC71 - 8944 - 62
55chain 'C' and (resid 90 through 110 )CC90 - 11063 - 83
66chain 'C' and (resid 111 through 118 )CC111 - 11884 - 91
77chain 'C' and (resid 119 through 141 )CC119 - 14192 - 114
88chain 'C' and (resid 142 through 154 )CC142 - 154115 - 127
99chain 'D' and (resid 2 through 8 )DD2 - 81 - 7
1010chain 'D' and (resid 9 through 21 )DD9 - 218 - 20
1111chain 'A' and (resid 28 through 35 )AA28 - 351 - 8
1212chain 'A' and (resid 36 through 45 )AA36 - 459 - 18
1313chain 'A' and (resid 46 through 62 )AA46 - 6219 - 35
1414chain 'A' and (resid 63 through 70 )AA63 - 7036 - 43
1515chain 'A' and (resid 71 through 89 )AA71 - 8944 - 62
1616chain 'A' and (resid 90 through 110 )AA90 - 11063 - 83
1717chain 'A' and (resid 111 through 118 )AA111 - 11884 - 91
1818chain 'A' and (resid 119 through 141 )AA119 - 14192 - 114
1919chain 'A' and (resid 142 through 155 )AA142 - 155115 - 128
2020chain 'B' and (resid 2 through 8 )BB2 - 81 - 7
2121chain 'B' and (resid 9 through 21 )BB9 - 218 - 20

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