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- PDB-5ixm: The LPS Transporter LptDE from Yersinia pestis, core complex -

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Basic information

Entry
Database: PDB / ID: 5ixm
TitleThe LPS Transporter LptDE from Yersinia pestis, core complex
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 / lipopolysaccharide binding / 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 speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.746 Å
AuthorsBotos, I. / Mayclin, S.J. / 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 23, 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 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / 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
C: LPS-assembly protein LptD
D: LPS-assembly lipoprotein LptE
E: LPS-assembly protein LptD
F: LPS-assembly lipoprotein LptE
G: LPS-assembly protein LptD
H: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,99829
Polymers349,5638
Non-polymers6,43521
Water9,728540
1
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9237
Polymers87,3912
Non-polymers1,5325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LPS-assembly protein LptD
D: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,14911
Polymers87,3912
Non-polymers2,7589
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-38 kcal/mol
Surface area34440 Å2
MethodPISA
3
E: LPS-assembly protein LptD
F: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6166
Polymers87,3912
Non-polymers1,2264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-34 kcal/mol
Surface area34710 Å2
MethodPISA
4
G: LPS-assembly protein LptD
H: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3105
Polymers87,3912
Non-polymers9193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-23 kcal/mol
Surface area33620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.892, 176.354, 143.848
Angle α, β, γ (deg.)90.00, 96.11, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a heterodimer formed by 1 LptD and 1 LptE molecule ( = core complex).

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Components

#1: Protein
LPS-assembly protein LptD


Mass: 65633.375 Da / Num. of mol.: 4 / Fragment: unp residues 225-780
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: lptD, imp, ostA, YPO0495, y3680, YP_3684 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZIK3
#2: Protein
LPS-assembly lipoprotein LptE


Mass: 21757.354 Da / Num. of mol.: 4 / Fragment: unp residues 21-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: lptE, rlpB, YPO2609, y1183, YP_1104 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CJV2
#3: Chemical...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM sodium cacodylate pH 6.5, 10% polyethelyene glycol (PEG) 2000, 15% PEG 6000

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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: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.746→40.129 Å / Num. obs: 106219 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.746→40.129 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 5378 5.06 %
Rwork0.2122 --
obs0.2147 106219 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.746→40.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21850 0 441 540 22831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422814
X-RAY DIFFRACTIONf_angle_d0.99830897
X-RAY DIFFRACTIONf_dihedral_angle_d13.3978419
X-RAY DIFFRACTIONf_chiral_restr0.0393272
X-RAY DIFFRACTIONf_plane_restr0.0053997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7459-2.77710.37351320.29542969X-RAY DIFFRACTION88
2.7771-2.80980.36192040.29823300X-RAY DIFFRACTION100
2.8098-2.84410.35251720.29113435X-RAY DIFFRACTION100
2.8441-2.880.33661810.27993355X-RAY DIFFRACTION100
2.88-2.91790.33881770.28153310X-RAY DIFFRACTION100
2.9179-2.95790.35491800.26893416X-RAY DIFFRACTION100
2.9579-3.00010.32021630.27333363X-RAY DIFFRACTION100
3.0001-3.04490.32981880.26183366X-RAY DIFFRACTION99
3.0449-3.09250.33761990.2523316X-RAY DIFFRACTION99
3.0925-3.14310.28631770.24033362X-RAY DIFFRACTION100
3.1431-3.19730.31211920.2383390X-RAY DIFFRACTION100
3.1973-3.25540.3031780.22893337X-RAY DIFFRACTION100
3.2554-3.3180.27931980.22633368X-RAY DIFFRACTION100
3.318-3.38570.27371580.21623371X-RAY DIFFRACTION100
3.3857-3.45930.27441570.22163429X-RAY DIFFRACTION100
3.4593-3.53970.27341740.20723357X-RAY DIFFRACTION100
3.5397-3.62820.25391670.20173374X-RAY DIFFRACTION100
3.6282-3.72620.2311930.19833331X-RAY DIFFRACTION100
3.7262-3.83580.28241790.19643400X-RAY DIFFRACTION100
3.8358-3.95950.25651770.19273399X-RAY DIFFRACTION100
3.9595-4.10090.2361930.19553354X-RAY DIFFRACTION100
4.1009-4.26490.25831610.18633400X-RAY DIFFRACTION100
4.2649-4.45870.22331780.1753380X-RAY DIFFRACTION100
4.4587-4.69350.17641640.15293408X-RAY DIFFRACTION100
4.6935-4.9870.17991920.1653372X-RAY DIFFRACTION100
4.987-5.37130.22081820.18113407X-RAY DIFFRACTION100
5.3713-5.91030.23331720.21743433X-RAY DIFFRACTION100
5.9103-6.7620.26861760.21623378X-RAY DIFFRACTION100
6.762-8.5060.27412200.21553384X-RAY DIFFRACTION100
8.506-40.13360.20761940.20373377X-RAY DIFFRACTION98

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