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- PDB-5iv9: The LPS Transporter LptDE from Klebsiella pneumoniae, full-length -

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Basic information

Entry
Database: PDB / ID: 5iv9
TitleThe LPS Transporter LptDE from Klebsiella pneumoniae, full-length
Components
  • LPS-assembly lipoprotein LptE
  • LPS-assembly protein LptD
KeywordsTRANSPORT PROTEIN / LptD / LptE / lipopolysaccharide / Transporter
Function / homology
Function and homology information


lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / : / cell outer membrane
Similarity search - Function
LptD, C-terminal / LPS-assembly protein LptD / LPS transport system D / Lipopolysaccharide-assembly / LPS-assembly lipoprotein LptE / 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 speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.369 Å
AuthorsBotos, I. / McCarthy, J.G. / 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

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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)105,9984
Polymers105,3852
Non-polymers6132
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-7 kcal/mol
Surface area45400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.219, 155.459, 197.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein LPS-assembly protein LptD


Mass: 85991.914 Da / Num. of mol.: 1 / Fragment: unp residues 25-782
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: imp, lptD / Production host: Escherichia coli (E. coli) / References: UniProt: C4T9I0
#2: Protein LPS-assembly lipoprotein LptE


Mass: 19392.877 Da / Num. of mol.: 1 / Fragment: unp residues 20-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: lptE, APU20_03225 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J4W1Y0
#3: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM

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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: 4.78 Å3/Da / Density % sol: 74.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 25% 1,2-propanediol, 100 mM phosphate-citrate pH 4.2, 10% glycerol, 5% PEG 3000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.369→44.717 Å / Num. obs: 12420 / % possible obs: 95.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.369→44.717 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3437 547 5.01 %
Rwork0.3014 --
obs0.3035 10921 81.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.369→44.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7242 0 42 0 7284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037455
X-RAY DIFFRACTIONf_angle_d0.63110120
X-RAY DIFFRACTIONf_dihedral_angle_d10.3222733
X-RAY DIFFRACTIONf_chiral_restr0.0231066
X-RAY DIFFRACTIONf_plane_restr0.0031339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3692-4.80850.3146970.28611822X-RAY DIFFRACTION58
4.8085-5.50320.35061270.30062402X-RAY DIFFRACTION76
5.5032-6.92930.38791510.34682866X-RAY DIFFRACTION90
6.9293-44.71910.33011720.28533284X-RAY DIFFRACTION99

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