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- PDB-4nhr: Crystal structure of the outer membrane lipopolysaccharide transp... -

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Basic information

Entry
Database: PDB / ID: 4nhr
TitleCrystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB)
ComponentsLPS-assembly lipoprotein LptE
KeywordsLIPID BINDING PROTEIN / 2-Layer Sandwich / lipopolysaccharide assembly / LptD (Imp) / lysine methylation / Gram-negative outer membrane
Function / homology
Function and homology information


transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / lipopolysaccharide binding / cell outer membrane
Similarity search - Function
Lipoprotein like domain / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Double Stranded RNA Binding Domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / LPS-assembly lipoprotein LptE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.34 Å
AuthorsMalojcic, G. / Kahne, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: LptE binds to and alters the physical state of LPS to catalyze its assembly at the cell surface.
Authors: Malojcic, G. / Andres, D. / Grabowicz, M. / George, A.H. / Ruiz, N. / Silhavy, T.J. / Kahne, D.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9812
Polymers18,8751
Non-polymers1061
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LPS-assembly lipoprotein LptE
hetero molecules

A: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9614
Polymers37,7492
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area3430 Å2
ΔGint-9 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.670, 87.670, 104.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-437-

HOH

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Components

#1: Protein LPS-assembly lipoprotein LptE / Rare lipoprotein B


Mass: 18874.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0641, JW0636, lptE, rlpB / Plasmid: pet22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ADC1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.0759.89
23.0759.89
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris/HOAc pH 8.5, 200 mM KBr, 10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9789
SYNCHROTRONNSLS X2520.9789
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMar 25, 2011
DECTRIS PILATUS 6M2PIXELMar 25, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1si111SINGLE WAVELENGTHMx-ray1
2si111SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
21
ReflectionResolution: 2.17→61.395 Å / Num. all: 10521 / Num. obs: 10493 / % possible obs: 100 % / Observed criterion σ(F): 0.85 / Observed criterion σ(I): 0.7 / Biso Wilson estimate: 67.66 Å2 / Net I/σ(I): 19.3
Reflection shellResolution: 2.34→61.4 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.34→43.003 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 31.06 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 496 4.73 %random
Rwork0.226 ---
all0.2272 10481 --
obs0.2272 10481 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→43.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 7 46 1129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081095
X-RAY DIFFRACTIONf_angle_d1.1261471
X-RAY DIFFRACTIONf_dihedral_angle_d17.439436
X-RAY DIFFRACTIONf_chiral_restr0.038169
X-RAY DIFFRACTIONf_plane_restr0.005192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.57550.32621100.30262451X-RAY DIFFRACTION100
2.5755-2.94810.30921360.27712421X-RAY DIFFRACTION100
2.9481-3.7140.29041370.25822473X-RAY DIFFRACTION100
3.714-43.01050.21221130.19822640X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.38962.0462-1.71970.90730.67413.2352-0.6719-1.27860.87210.00720.02190.8102-1.67140.9303-0.22261.23970.422-0.30920.7832-0.35560.886712.453838.269357.0366
24.4091-1.13832.02935.77723.62784.1553-1.0144-1.90190.5391.42411.0665-0.98280.67232.78520.08720.89980.1471-0.33661.317-0.02790.835624.026927.303752.8052
32.52990.4522.43797.43416.24186.991-0.1982-0.47061.15821.65010.189-1.61390.00381.3016-0.63461.27570.0141-0.3270.8334-0.01151.084118.757936.598754.2677
46.98921.45251.85678.7151-1.82261.9462-0.7238-1.7517-0.00463.4278-0.16881.39732.2426-0.16960.79140.99490.1045-0.06210.8914-0.0340.568914.350226.778958.0379
57.1029-0.4809-0.01413.2619-0.40556.6190.02490.2728-0.7673-0.5584-0.43110.19662.15991.08980.1641.05630.4004-0.15140.64870.04230.530220.334915.642635.7676
65.73260.7727-1.13586.7255-1.65174.9469-0.3266-0.32130.24090.5987-0.20060.58031.26-0.75520.05410.5785-0.0021-0.0560.7321-0.16640.532610.084522.584847.427
76.3172-2.6139-6.86348.18274.19377.76271.11360.03441.53280.58980.151-2.0592-0.32893.7606-1.01240.65590.29840.02071.56020.15911.019230.10922.44927.6653
82.9857-2.4903-1.73073.78275.10228.64050.83620.97530.1767-1.0321-0.00010.3522-0.52440.5942-0.3850.58810.0255-0.09890.68550.03870.547422.358726.569140.3795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 33:37)
2X-RAY DIFFRACTION2(chain A and resid 38:51)
3X-RAY DIFFRACTION3(chain A and resid 52:66)
4X-RAY DIFFRACTION4(chain A and resid 67:82)
5X-RAY DIFFRACTION5(chain A and resid 83:112)
6X-RAY DIFFRACTION6(chain A and resid 113:124)
7X-RAY DIFFRACTION7(chain A and resid 125:143)
8X-RAY DIFFRACTION8(chain A and resid 144:152)

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