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- PDB-6xlp: Structure of the essential inner membrane lipopolysaccharide-PbgA... -

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Basic information

Entry
Database: PDB / ID: 6xlp
TitleStructure of the essential inner membrane lipopolysaccharide-PbgA complex
ComponentsLPS binding protein
KeywordsLIPID BINDING PROTEIN / lipopolysaccharide / LPS / membrane protein
Function / homology
Function and homology information


Inner membrane protein YejM / Inner membrane protein YejM, N-terminal / : / Domain of unknown function (DUF3413) / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Inner membrane protein YejM / Inner membrane protein YejM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPayandeh, J. / Clairefeuille, T.
CitationJournal: Nature / Year: 2020
Title: Structure of the essential inner membrane lipopolysaccharide-PbgA complex.
Authors: Clairfeuille, T. / Buchholz, K.R. / Li, Q. / Verschueren, E. / Liu, P. / Sangaraju, D. / Park, S. / Noland, C.L. / Storek, K.M. / Nickerson, N.N. / Martin, L. / Dela Vega, T. / Miu, A. / ...Authors: Clairfeuille, T. / Buchholz, K.R. / Li, Q. / Verschueren, E. / Liu, P. / Sangaraju, D. / Park, S. / Noland, C.L. / Storek, K.M. / Nickerson, N.N. / Martin, L. / Dela Vega, T. / Miu, A. / Reeder, J. / Ruiz-Gonzalez, M. / Swem, D. / Han, G. / DePonte, D.P. / Hunter, M.S. / Gati, C. / Shahidi-Latham, S. / Xu, M. / Skelton, N. / Sellers, B.D. / Skippington, E. / Sandoval, W. / Hanan, E.J. / Payandeh, J. / Rutherford, S.T.
History
DepositionJun 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LPS binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,88922
Polymers68,4921
Non-polymers6,39721
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.272, 56.328, 97.359
Angle α, β, γ (deg.)90.000, 106.450, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein LPS binding protein / DUF3413 domain-containing protein / Hydrolase of alkaline phosphatase superfamily / Hydrolase / ...DUF3413 domain-containing protein / Hydrolase of alkaline phosphatase superfamily / Hydrolase / inner membrane / Inner membrane protein YejM / Membrane protein / Putative hydrolase / Putative sulfatase / Sulfatase


Mass: 68491.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yejM, pbgA, yejM_2 / Production host: Escherichia coli (E. coli) / References: UniProt: C3T3G2, UniProt: P0AD27*PLUS
#2: Polysaccharide 2-deoxy-3-O-[(1R,3R)-1,3-dihydroxytetradecyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono- ...2-deoxy-3-O-[(1R,3R)-1,3-dihydroxytetradecyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-alpha-D-glucopyranose-(6-1)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)]1,5-anhydro-2-deoxy-2-{[(1S,3R)-1-hydroxy-3-(pentanoyloxy)undecyl]amino}-4-O-phosphono-D-glucitol


Type: oligosaccharide / Mass: 1445.598 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1a_1-5_1*OPO/3O/3=O_2*NCCC^RCCCCCCCCCCC/5O/3=O_3*OC^RCC^RCCCCCCCCCCC/5O/3O][a2122h-1a_1-5_2*NC^SCC^ROCCCCC/7=O/5CCCCCCCC/3O_4*OPO/3O/3=O][Aad1122h-2a_2-6]/1-2-3/a6-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][P]{[(0+1)][a-D-GlcpN]{[(2+1)][<C14O2>]{}[(3+1)][<C14O2>]{}[(6+1)][b-D-GlcpN]{[(2+1)][<C16O3>]{}[(4+0)][P]{}[(6+2)][a-D-Kdop]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 166 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 8
Details: LCP was formulated from monoolein (Sigma): phosphatidylethanolamine (E. coli PE, Avanti Polar Lipids) 99.5:0.5% m/m mixture at 40% hydration; crystallization solution contained 0.1 M Tris pH ...Details: LCP was formulated from monoolein (Sigma): phosphatidylethanolamine (E. coli PE, Avanti Polar Lipids) 99.5:0.5% m/m mixture at 40% hydration; crystallization solution contained 0.1 M Tris pH 8.0, 0.2 M ammonium sulfate, 40% PEG200
Temp details: room temperature

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→24.242 Å / Num. obs: 53215 / % possible obs: 88 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3926 / CC1/2: 0.741 / % possible all: 62.1

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Processing

Software
NameVersionClassification
PHENIXDEV_2747refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I5H

5i5h


Resolution: 2→24.24 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 1791 3.37 %
Rwork0.193 51424 -
obs0.194 53215 88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138 Å2 / Biso mean: 51.56 Å2 / Biso min: 20.65 Å2
Refinement stepCycle: final / Resolution: 2→24.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 342 146 5160
Biso mean--77.68 48.1 -
Num. residues----586
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.05410.30671000.271287964
2.0541-2.11450.2631090.253311170
2.1145-2.18270.2891180.2379338276
2.1827-2.26060.24271240.2267355279
2.2606-2.35110.26461290.2203374184
2.3511-2.4580.23251440.2202412492
2.458-2.58740.2321480.2033426195
2.5874-2.74930.22171480.1929428196
2.7493-2.96130.20891520.185434296
2.9613-3.25860.2241530.189439098
3.2586-3.72870.18131530.1825438897
3.7287-4.69220.19431560.1745446999
4.6922-24.240.19731570.1884450497
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)
10.9444-0.33660.41021.6903-1.04613.2777-0.0236-0.0265-0.04470.1550.03240.07990.0976-0.0261-0.01720.26710.00660.00650.1311-0.02310.24455.67232.65986.284
21.4967-0.1893-0.09232.16-0.36452.21490.03660.3136-0.0709-0.1722-0.0510.24750.07190.11460.0190.2316-0.0049-0.01050.4701-0.05590.304310.8832.11542.619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:246 )A1 - 246
2X-RAY DIFFRACTION2( CHAIN A AND RESID 247:586 )A247 - 586

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