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- PDB-8h1r: Crystal structure of LptDE-YifL complex -

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Basic information

Entry
Database: PDB / ID: 8h1r
TitleCrystal structure of LptDE-YifL complex
Components
  • LPS-assembly lipoprotein LptE
  • LPS-assembly protein LptD
  • Uncharacterized lipoprotein YifL
KeywordsMEMBRANE PROTEIN / Lipopolysaccharide / Lipoprotein / LptDE
Function / homology
Function and homology information


regulation of polysaccharide biosynthetic process / transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / lipopolysaccharide binding
Similarity search - Function
Prokaryotic lipoprotein-attachment site / LPS-assembly lipoprotein LptM, conserved region / LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-PCJ / LPS-assembly lipoprotein LptM / LPS-assembly lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsLuo, Q. / Huang, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500404 China
Chinese Academy of SciencesXDB37020201 China
National Natural Science Foundation of China (NSFC)31625009 China
CitationJournal: Nat Commun / Year: 2025
Title: Surface lipoprotein sorting by crosstalk between Lpt and Lol pathways in gram-negative bacteria
Authors: Luo, Q. / Wang, C. / Qiao, S. / Yu, S. / Chen, L. / Kim, S. / Wang, K. / Zheng, J. / Zhang, Y. / Wu, F. / Lei, X. / Lou, J. / Hennig, M. / Im, W. / Miao, L. / Zhou, M. / Bei, W. / Huang, Y.
History
DepositionOct 3, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
C: Uncharacterized lipoprotein YifL
D: LPS-assembly protein LptD
E: LPS-assembly lipoprotein LptE
F: Uncharacterized lipoprotein YifL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,7548
Polymers268,9616
Non-polymers1,7932
Water00
1
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
C: Uncharacterized lipoprotein YifL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,3774
Polymers134,4813
Non-polymers8961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-24 kcal/mol
Surface area44400 Å2
MethodPISA
2
D: LPS-assembly protein LptD
E: LPS-assembly lipoprotein LptE
F: Uncharacterized lipoprotein YifL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,3774
Polymers134,4813
Non-polymers8961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-25 kcal/mol
Surface area46810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.848, 140.475, 133.180
Angle α, β, γ (deg.)90.000, 104.390, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein LPS-assembly protein LptD


Mass: 104387.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: lptD, imp, ostA, PA0595 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I5U2
#2: Protein LPS-assembly lipoprotein LptE


Mass: 22908.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: lptE, PA3988 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HX32
#3: Protein Uncharacterized lipoprotein YifL


Mass: 7184.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: yifL, b4558, JW3781 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADN6
#4: Chemical ChemComp-PCJ / (2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE


Mass: 896.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C54H105NO6S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 175 mM citric acid/Bis-Tris (pH 5.0), 17% (v/v) PEG3350 and 3% methanol (as additive)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.98→43.25 Å / Num. obs: 66447 / % possible obs: 97.28 % / Redundancy: 5 % / Biso Wilson estimate: 72.3 Å2 / CC1/2: 0.92 / Net I/σ(I): 7.3
Reflection shellResolution: 2.98→3.09 Å / Num. unique obs: 6661 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IVA

5iva


Resolution: 2.98→43.25 Å / SU ML: 0.3795 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8716
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264 3322 5 %
Rwork0.234 63125 -
obs0.2355 66447 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.91 Å2
Refinement stepCycle: LAST / Resolution: 2.98→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15225 0 229 0 15454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010515792
X-RAY DIFFRACTIONf_angle_d1.271321318
X-RAY DIFFRACTIONf_chiral_restr0.05752214
X-RAY DIFFRACTIONf_plane_restr0.00992809
X-RAY DIFFRACTIONf_dihedral_angle_d14.34345938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.020.3418640.30211221X-RAY DIFFRACTION45.01
3.02-3.070.34461390.31772647X-RAY DIFFRACTION98.97
3.07-3.120.34571440.31052706X-RAY DIFFRACTION99.86
3.12-3.170.34471390.29842672X-RAY DIFFRACTION99.89
3.17-3.220.33331420.29652691X-RAY DIFFRACTION99.96
3.22-3.280.2951420.28532699X-RAY DIFFRACTION99.82
3.28-3.340.30461420.26162697X-RAY DIFFRACTION99.96
3.34-3.410.26281410.24362694X-RAY DIFFRACTION99.96
3.41-3.480.27381410.24272677X-RAY DIFFRACTION99.79
3.49-3.570.27861420.24922681X-RAY DIFFRACTION99.86
3.57-3.660.32011430.26622704X-RAY DIFFRACTION99.34
3.66-3.750.33721380.28092679X-RAY DIFFRACTION98.95
3.75-3.860.29531400.24542659X-RAY DIFFRACTION99.82
3.86-3.990.25671430.24222699X-RAY DIFFRACTION99.75
3.99-4.130.26631430.24382720X-RAY DIFFRACTION99.79
4.13-4.30.27651430.22772707X-RAY DIFFRACTION99.86
4.3-4.490.22921420.22699X-RAY DIFFRACTION99.82
4.49-4.730.1961400.18842679X-RAY DIFFRACTION99.44
4.73-5.020.25551420.19732694X-RAY DIFFRACTION99.54
5.02-5.410.22261430.21322708X-RAY DIFFRACTION99.65
5.41-5.960.2271410.22122696X-RAY DIFFRACTION99.65
5.96-6.810.27681440.23612712X-RAY DIFFRACTION99.48
6.81-8.570.24971430.21872733X-RAY DIFFRACTION99.93
8.57-43.250.24121410.21542651X-RAY DIFFRACTION95.03
Refinement TLS params.Method: refined / Origin x: 50.8840406695 Å / Origin y: 116.448558865 Å / Origin z: 162.750299177 Å
111213212223313233
T0.435669160748 Å2-0.0164662517992 Å2-0.03954630523 Å2-0.4532717688 Å2-0.00864451099578 Å2--0.525459960555 Å2
L0.215485045132 °2-0.0655090389195 °2-0.217689716977 °2-0.216892639455 °20.0552424874841 °2--0.703078504888 °2
S-0.014916589982 Å °-0.0356959912878 Å °0.0430682506253 Å °0.0240206975374 Å °0.0297115183839 Å °-0.0212059567925 Å °0.144285790121 Å °-0.00305154556085 Å °0.0040162373137 Å °
Refinement TLS groupSelection details: all

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