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- PDB-8gal: Crystal Structure of the E. coli LptA in complex with Murgantia h... -

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Basic information

Entry
Database: PDB / ID: 8gal
TitleCrystal Structure of the E. coli LptA in complex with Murgantia histrionica 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 / cell outer membrane / lipopolysaccharide binding / outer membrane-bounded periplasmic space
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Murgantia histrionica (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKibrom, A. / Huynh, K. / 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 1.1Nov 20, 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)33,4804
Polymers33,4804
Non-polymers00
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-27 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.600, 62.470, 147.120
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: 2203.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murgantia histrionica (insect) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25 mM Tris pH 8.5, 100 mM NaCl, 0.0475 M sodium citrate pH 5.6, 9.5% isopropanol, 9.5% PEG 4000, 2.5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→47.62 Å / Num. obs: 39095 / % possible obs: 97.89 % / Redundancy: 5.5 % / Biso Wilson estimate: 30.62 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 14.17
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 3874 / CC1/2: 0.936 / CC star: 0.983

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.62 Å / SU ML: 0.2238 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.4563
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2123 1944 4.98 %
Rwork0.1814 37086 -
obs0.183 39030 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 0 334 2557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01532311
X-RAY DIFFRACTIONf_angle_d1.36913134
X-RAY DIFFRACTIONf_chiral_restr0.0982356
X-RAY DIFFRACTIONf_plane_restr0.0103419
X-RAY DIFFRACTIONf_dihedral_angle_d5.6443318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.32421370.27072635X-RAY DIFFRACTION98.47
1.84-1.890.3081360.24742645X-RAY DIFFRACTION98.79
1.89-1.950.28411380.22352615X-RAY DIFFRACTION98.78
1.95-2.010.31861380.24932616X-RAY DIFFRACTION98.67
2.01-2.090.28431390.22382651X-RAY DIFFRACTION98.38
2.09-2.170.26051380.20022629X-RAY DIFFRACTION98.33
2.17-2.270.25241360.18912612X-RAY DIFFRACTION98.35
2.27-2.390.22731390.18552647X-RAY DIFFRACTION98.45
2.39-2.540.2391400.19772666X-RAY DIFFRACTION98.59
2.54-2.730.23571380.18492640X-RAY DIFFRACTION98.44
2.73-3.010.22241400.18922673X-RAY DIFFRACTION98.01
3.01-3.440.19941390.18032637X-RAY DIFFRACTION96.72
3.44-4.340.17521380.15142645X-RAY DIFFRACTION95.54
4.34-47.620.17031480.16312775X-RAY DIFFRACTION95.24
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)
17.82870287696-1.614266966437.721295795693.84007194632-3.90347630699.767368183940.2144335400420.527299195220.0329294937882-0.3150673146430.176159308678-0.1877481524290.3386321385080.931583351104-0.3032274794490.203137313160.03886507026840.02499824519710.43705739823-0.0342226875940.26550417961911.77538705863.73850045964.3257881564
27.0620550385-3.501234555233.308574659855.515031377260.1739725034922.43806642408-0.123901535350.1083928272140.1219967088520.447992058647-0.0591337930808-0.033904817168-0.4985970136330.05229767688320.1679555682980.22578635508-0.03691897835580.01545866808160.218703794311-0.00224087888690.25088207478613.66379764233.5393378260824.4782414386
34.43770053131-0.4503508000660.8229461988133.67292778515-0.5964279861767.654406706430.1484202755850.124981350909-0.3723595380360.1524526264240.165418158179-0.08911197823580.5151987682570.30402241714-0.260315056920.1792478781590.0027547636209-0.02977964122830.233165745355-0.01982526696740.20776128643112.2356683541-1.4755829298423.298635705
44.47161991809-0.111304642490.2435401241492.98143475017-1.002059371457.241883399950.1023930163980.0932162439065-0.3444271782260.3605547476810.07988181701070.1442495568920.373930176162-0.252051468427-0.1719337892030.202476324294-0.0496606137666-0.01508722725350.214202052157-0.03357764356170.2351444025588.39031902634-0.85320603462618.5497473916
54.32425939801-4.40525477239-5.634813029758.681358596733.357570480328.94599604277-0.006767172246950.237438621786-0.76966702404-0.2043815398260.08656641714690.01653115516411.179268377980.292245126102-0.08347255938780.4706677979590.0267408828487-0.1199994775730.416473720634-0.07415220388610.36913271743310.239186417-7.5084945592616.0971421643
62.341693594580.825528900167-1.482676254992.43931755157-2.277867817222.37388938280.05969406789640.2973170013170.0640431379967-0.02592064556610.09551679244630.102843259087-0.0925758727951-0.86137930291-0.1641345427310.2108964892130.02296043724820.008372903908620.3906802608640.01687107771210.275855070424-1.329089206867.7331969270610.1166746878
75.590157966660.965283257703-1.352120664713.20551968786-0.3478089483586.171694669940.1781937048580.236396570726-0.254833123616-0.1971812414570.1684174802810.1978935422140.58271801655-0.48590391734-0.2983650006620.326709817867-0.0545905095003-0.07816635831820.2624456910740.01100015266510.3055537741421.89850455444-4.7219290646912.0385041027
81.337842249161.10935990224-1.288717163894.39499413011-5.404042454516.656132656920.3184870483770.00586067573883-0.3481080356560.1895865589090.3318053442620.936020371219-0.382615775848-0.961180898229-0.6081619789450.2675959901670.02566740736480.04070150877860.5735436836690.09285181899670.436147713254-9.163955558754.0174910232213.3428939007
93.205312316830.0757642086237-0.7449278177159.64896717144.850605939765.878995796160.3002035754340.08599152688180.117648489136-0.353772514462-0.322303908339-0.578297712012-0.5922494481170.7932965663590.03285895054760.282528887549-0.1108819744230.01176169182460.5022446375730.08122573026170.308495519118-5.9713051624224.2921273879.50882181101
103.84415373334-2.880922887674.460789153875.89136277848-4.971320458269.535685712440.4938019798890.159284520338-0.344397412532-0.164774543738-0.004873693807330.739172558026-0.21343692799-0.299181079624-0.432279219380.3034432346150.118214944150.04508891752070.4818260830280.01241208050830.330917988642-25.052433531929.32039311413.34979033062
116.983144713521.067224072840.3550075773249.299288206686.630407895874.817041356860.4930843342190.350292355422-0.353055930489-0.672727066736-0.323835919721-0.185106101965-0.2758752501020.195011132894-0.1430040155860.3569372808710.142535094674-0.03231826080030.375311662872-0.008284409078460.28016801159717.76267168560.024348925726114.1396544055
126.634942628520.53919020821.648736181777.83091793830.6782939298545.876728923360.4179659977370.359180314736-0.1888499926310.174047255816-0.163369557113-0.5423583303270.1197859300590.590354243415-0.2496524871110.2298871031740.0206990809153-0.03129783913050.2663194401410.02042035655370.27574916646919.50039990675.6659765768524.4602965887
132.122828847740.2465852458670.2958371604331.844644076051.426630536875.61995741940.2062788294320.0857250223746-0.08325991744760.352644666572-0.0210718933608-0.01034002502940.224168367598-0.0825000531481-0.1653243544190.277442178978-0.02182473134270.009503165348020.18345262750.02560685529230.305513298847-22.241974703218.877904340727.8464146362
141.17858079690.04745253103150.1778080519521.133023598771.028728506616.191015697440.01299573550820.1193081344150.07583290770960.00573499144291-0.0118070949875-0.0638792121537-0.5602468692390.188246713086-0.02193365157510.265471320343-0.0428562716796-0.02100375869740.1946224719380.01597800264640.262142899954-17.053355763124.307732253623.7561546925
150.432829733108-1.73237914640.02667741665417.474860320240.7232688822061.037490974780.252126442220.0813436754161-0.193894383501-0.255194557792-0.2722734299270.5341769885490.108212015448-0.2369650344470.01411149715750.233258432092-0.0722537442379-0.0154389139170.5258864482460.00316609495610.375251603516-9.0111392146610.62818226311.0964907939
162.106486663591.28019162475-1.049506355763.65993318563-0.8265839051885.150840855720.0820796956526-0.0660111559531-0.00192048993175-0.444195315768-0.272852492392-0.1729230230350.5371147848190.8647016431080.1704756303420.3571875954670.10689223119-0.02589277727450.477877725110.03207178269450.2934846538457.58658140056-0.0175678838592-3.01391800548
172.01367277252-0.9758582853221.845015670938.427181472090.3933730267959.826105175160.4251369714130.05908457238630.00140568166744-0.128515987854-0.3750028864120.62513678955-0.125713517823-0.537790478499-0.06696259041490.3374503448190.06528596059780.07904433174340.2913583841620.01254815052670.361070281759-28.006230864321.149703320828.5158232808
187.89143399063-5.187989970862.255555653518.43888838575-2.562085382568.25445840925-0.0744088375984-0.897008984346-0.06842271305680.9879793145440.4038059214750.167864641876-0.540187863535-0.662963491575-0.3974957539470.521392857575-0.005764800760340.06800416281480.3534736198790.03166690257860.368378311886-22.808180353314.844928327837.3826170075
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 35 )AA28 - 351 - 8
22chain 'A' and (resid 36 through 45 )AA36 - 459 - 18
33chain 'A' and (resid 46 through 62 )AA46 - 6219 - 35
44chain 'A' and (resid 63 through 79 )AA63 - 7936 - 52
55chain 'A' and (resid 80 through 89 )AA80 - 8953 - 62
66chain 'A' and (resid 90 through 109 )AA90 - 10963 - 82
77chain 'A' and (resid 110 through 124 )AA110 - 12483 - 97
88chain 'A' and (resid 125 through 131 )AA125 - 13198 - 104
99chain 'A' and (resid 132 through 141 )AA132 - 141105 - 114
1010chain 'A' and (resid 142 through 155 )AA142 - 155115 - 128
1111chain 'B' and (resid 4 through 11 )BB4 - 111 - 8
1212chain 'B' and (resid 12 through 21 )BB12 - 219 - 18
1313chain 'C' and (resid 28 through 45 )CC28 - 451 - 18
1414chain 'C' and (resid 46 through 124 )CC46 - 12419 - 97
1515chain 'C' and (resid 125 through 141 )CC125 - 14198 - 114
1616chain 'C' and (resid 142 through 155 )CC142 - 155115 - 128
1717chain 'D' and (resid 4 through 11 )DD4 - 111 - 8
1818chain 'D' and (resid 12 through 21 )DD12 - 219 - 18

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