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- PDB-5iva: The LPS Transporter LptDE from Pseudomonas aeruginosa, core complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5iva
TitleThe LPS Transporter LptDE from Pseudomonas aeruginosa, core complex
Components
  • LPS-assembly lipoprotein LptE
  • LPS-assembly protein LptD
KeywordsTRANSPORT PROTEIN / LptD / LptE / lipopolysaccharide / Transporter
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 lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.988 Å
AuthorsBotos, I. / Buchanan, S.K.
CitationJournal: Structure / Year: 2016
Title: Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.
Authors: Botos, I. / Majdalani, N. / Mayclin, S.J. / McCarthy, J.G. / Lundquist, K. / Wojtowicz, D. / Barnard, T.J. / Gumbart, J.C. / Buchanan, S.K.
History
DepositionMar 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8959
Polymers96,7502
Non-polymers2,1457
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint3 kcal/mol
Surface area35830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.923, 155.985, 115.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein LPS-assembly protein LptD


Mass: 75433.367 Da / Num. of mol.: 1 / Fragment: unp residues 300-924
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: lptD, imp, ostA, PA0595 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I5U2
#2: Protein LPS-assembly lipoprotein LptE


Mass: 21316.590 Da / Num. of mol.: 1 / Fragment: unp residues 21-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lptE, PAMH19_1038 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A8RAG8, UniProt: Q9HX32*PLUS
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 3.47 Å3/Da / Density % sol: 64.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium citrate pH 5.5, 100 mM sodium chloride, 100 mM lithium chloride, 12% PEG 4000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.988→49.089 Å / Num. obs: 27493 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q35

4q35


Resolution: 2.988→49.089 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2954 1384 5.03 %
Rwork0.2479 --
obs0.2502 27493 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.988→49.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5953 0 147 4 6104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036237
X-RAY DIFFRACTIONf_angle_d0.6688404
X-RAY DIFFRACTIONf_dihedral_angle_d12.9712381
X-RAY DIFFRACTIONf_chiral_restr0.026859
X-RAY DIFFRACTIONf_plane_restr0.0041102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9883-3.0950.39341640.37092436X-RAY DIFFRACTION96
3.095-3.21890.39051450.33542560X-RAY DIFFRACTION100
3.2189-3.36540.35951290.31112607X-RAY DIFFRACTION100
3.3654-3.54280.35821340.29012595X-RAY DIFFRACTION100
3.5428-3.76470.29981340.26082615X-RAY DIFFRACTION100
3.7647-4.05520.29011240.2712631X-RAY DIFFRACTION100
4.0552-4.46310.29741260.2292626X-RAY DIFFRACTION100
4.4631-5.10830.24151470.20342627X-RAY DIFFRACTION100
5.1083-6.43370.27811430.22732644X-RAY DIFFRACTION100
6.4337-49.09570.2721380.22252768X-RAY DIFFRACTION100

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