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- PDB-8h1s: Crystal structure of apo-LptDE complex -

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Basic information

Entry
Database: PDB / ID: 8h1s
TitleCrystal structure of apo-LptDE complex
Components
  • LPS-assembly lipoprotein LptE
  • LPS-assembly protein LptD
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
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
LPS-assembly lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsLuo, Q. / Huang, Y.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesCAS201973 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 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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

Downloads & links

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Assembly

Deposited unit
C: LPS-assembly protein LptD
D: LPS-assembly lipoprotein LptE
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE


Theoretical massNumber of molelcules
Total (without water)254,5934
Polymers254,5934
Non-polymers00
Water00
1
C: LPS-assembly protein LptD
D: LPS-assembly lipoprotein LptE


Theoretical massNumber of molelcules
Total (without water)127,2962
Polymers127,2962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint4 kcal/mol
Surface area46840 Å2
MethodPISA
2
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE


Theoretical massNumber of molelcules
Total (without water)127,2962
Polymers127,2962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint2 kcal/mol
Surface area47570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.027, 160.485, 218.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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) / Variant (production host): delta yifl / 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) / Variant (production host): delta yifl / References: UniProt: Q9HX32
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: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 2% tacsimate (pH5.0), 16% PEG3350, 100mM sodium citrate tribasic dehydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2016
RadiationMonochromator: 0.9792 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 65178 / % possible obs: 96.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 80.81 Å2 / Rmerge(I) obs: 0.674 / Rpim(I) all: 0.38 / Rrim(I) all: 0.742 / Χ2: 1.563 / Net I/σ(I): 5.2 / Num. measured all: 354588
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.2-3.315.462170.0184.7241.11393.8
3.31-3.455.462730.0492.6431.21593.95.8096.401
3.45-3.65.463060.1911.9811.29394.54.3594.803
3.6-3.795.363620.371.1651.43952.5622.823
3.79-4.035.364540.6330.841.5996.41.852.038
4.03-4.345.465480.8580.3371.6797.50.7450.82
4.34-4.785.566410.9660.1631.75998.60.360.396
4.78-5.475.767030.9730.1281.721990.2850.313
5.47-6.895.867440.9820.1021.84198.90.2280.251
6.89-505.269300.9970.0341.88797.30.0720.08

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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: 3.28→43.09 Å / SU ML: 0.4423 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.0093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 2952 5 %
Rwork0.2421 56064 -
obs0.2439 59016 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.38 Å2
Refinement stepCycle: LAST / Resolution: 3.28→43.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15858 0 0 0 15858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016216215
X-RAY DIFFRACTIONf_angle_d1.212321977
X-RAY DIFFRACTIONf_chiral_restr0.05982304
X-RAY DIFFRACTIONf_plane_restr0.00942931
X-RAY DIFFRACTIONf_dihedral_angle_d13.48656009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.340.391220.33322329X-RAY DIFFRACTION84.72
3.34-3.40.34931350.32882558X-RAY DIFFRACTION94.56
3.4-3.460.35321350.31532563X-RAY DIFFRACTION93.16
3.46-3.520.32091360.29472578X-RAY DIFFRACTION94.43
3.52-3.60.28941350.28612554X-RAY DIFFRACTION94.68
3.6-3.670.34291370.28592613X-RAY DIFFRACTION94.89
3.67-3.760.29821400.28582652X-RAY DIFFRACTION96.04
3.76-3.850.29441360.2732605X-RAY DIFFRACTION96.14
3.85-3.960.31141410.27472666X-RAY DIFFRACTION96.69
3.96-4.070.30541400.25512682X-RAY DIFFRACTION97.75
4.07-4.210.29691430.24522697X-RAY DIFFRACTION97.66
4.21-4.360.28131430.23132724X-RAY DIFFRACTION98.66
4.36-4.530.23921430.212713X-RAY DIFFRACTION99.06
4.53-4.740.23581430.18972738X-RAY DIFFRACTION98.9
4.74-4.990.22811440.2042730X-RAY DIFFRACTION98.97
4.99-5.30.25451450.21442735X-RAY DIFFRACTION98.87
5.3-5.710.24051450.22582762X-RAY DIFFRACTION98.94
5.71-6.280.26881460.24442768X-RAY DIFFRACTION98.78
6.28-7.180.2831450.25032769X-RAY DIFFRACTION98.78
7.18-9.040.26821480.23122800X-RAY DIFFRACTION98.23
9.04-43.090.27341500.21742828X-RAY DIFFRACTION95.24
Refinement TLS params.Method: refined / Origin x: 30.5890181511 Å / Origin y: 0.0902286188344 Å / Origin z: 436.209785728 Å
111213212223313233
T0.458840071136 Å20.0196831776342 Å2-0.0148543602029 Å2-0.573285452254 Å20.0025719389468 Å2--0.480038844596 Å2
L0.308692961952 °20.0800125056651 °2-0.0324695640473 °2-0.699159805466 °20.0561219698413 °2--0.119721309697 °2
S-0.000732222880448 Å °0.0435233044879 Å °0.0270596349359 Å °-0.0128639752761 Å °0.0152156233355 Å °0.0317571950933 Å °-0.0254716203488 Å °-0.0413428485512 Å °-0.0313159914695 Å °
Refinement TLS groupSelection details: all

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