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- PDB-5iv8: The LPS Transporter LptDE from Klebsiella pneumoniae, core complex -

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Basic information

Entry
Database: PDB / ID: 5iv8
TitleThe LPS Transporter LptDE from Klebsiella pneumoniae, core complex
Components
  • LPS biosynthesis protein
  • LPS-assembly lipoprotein LptE
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 / Lipoprotein like domain / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Double Stranded RNA Binding Domain ...LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / Lipoprotein like domain / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Double Stranded RNA Binding Domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
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: 2.938 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
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 biosynthesis protein
B: LPS-assembly lipoprotein LptE
C: LPS biosynthesis protein
D: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,40512
Polymers177,9534
Non-polymers2,4528
Water362
1
A: LPS biosynthesis protein
B: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8965
Polymers88,9772
Non-polymers9193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-15 kcal/mol
Surface area34600 Å2
MethodPISA
2
C: LPS biosynthesis protein
D: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5097
Polymers88,9772
Non-polymers1,5325
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-15 kcal/mol
Surface area33670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.020, 173.050, 84.757
Angle α, β, γ (deg.)90.00, 111.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LPS biosynthesis protein


Mass: 69113.391 Da / Num. of mol.: 2 / Fragment: unp residues 203-782
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: AU361_02400 / Plasmid: pJGM013 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U3IWD2, UniProt: C4T9I0*PLUS
#2: Protein LPS-assembly lipoprotein LptE


Mass: 19863.355 Da / Num. of mol.: 2 / Fragment: unp residues 20-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: lptE, APU20_03225, SM74_00486, SM87_01358 / Plasmid: pJGM030 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J4W1Y0
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% PEG4K, 200mM ammonium phosphate

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.938→46.58 Å / Num. obs: 41834 / % possible obs: 97.4 % / Redundancy: 4 % / Net I/σ(I): 16.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q35

4q35


Resolution: 2.938→41.414 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.18
RfactorNum. reflection% reflection
Rfree0.2839 1989 5.55 %
Rwork0.235 --
obs0.2378 35870 83.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.938→41.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11177 0 168 2 11347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211606
X-RAY DIFFRACTIONf_angle_d0.48815712
X-RAY DIFFRACTIONf_dihedral_angle_d13.1176884
X-RAY DIFFRACTIONf_chiral_restr0.0421640
X-RAY DIFFRACTIONf_plane_restr0.0042051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9377-3.01110.367360.3022737X-RAY DIFFRACTION25
3.0111-3.09250.3014520.29041069X-RAY DIFFRACTION37
3.0925-3.18350.33671220.29231599X-RAY DIFFRACTION57
3.1835-3.28620.3291250.28652239X-RAY DIFFRACTION77
3.2862-3.40360.35671490.27842611X-RAY DIFFRACTION90
3.4036-3.53980.37441550.2782753X-RAY DIFFRACTION96
3.5398-3.70080.32031710.27732780X-RAY DIFFRACTION97
3.7008-3.89580.33861660.25742784X-RAY DIFFRACTION97
3.8958-4.13960.27711670.23692838X-RAY DIFFRACTION98
4.1396-4.45890.2631640.19822875X-RAY DIFFRACTION99
4.4589-4.9070.21111740.17262861X-RAY DIFFRACTION100
4.907-5.61550.23931720.20622901X-RAY DIFFRACTION100
5.6155-7.06930.3141730.23762904X-RAY DIFFRACTION100
7.0693-41.41840.2371630.22682930X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 30.6673 Å / Origin y: -56.9339 Å / Origin z: -64.1474 Å
111213212223313233
T0.0962 Å2-0.2053 Å2-0.0617 Å2-0.0869 Å2-0.2196 Å2--0.0772 Å2
L0.0031 °2-0.0659 °2-0.0387 °2--0.021 °2-0.0915 °2--0.16 °2
S-0.003 Å °-0.0016 Å °-0.0199 Å °-0.1191 Å °0.086 Å °-0.0004 Å °0.121 Å °0.0084 Å °0.1372 Å °
Refinement TLS groupSelection details: all

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