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- PDB-6mit: LptBFGC from Enterobacter cloacae -

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Basic information

Entry
Database: PDB / ID: 6mit
TitleLptBFGC from Enterobacter cloacae
Components
  • (Lipopolysaccharide export system ...) x 3
  • LPS export ABC transporter permease LptF
KeywordsLIPID TRANSPORT / lipopolysaccharide transport / ABC-transporter
Function / homology
Function and homology information


lipopolysaccharide transmembrane transporter activity / glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / : / Lipopolysaccharide-assembly, LptC-related / Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter ...Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / : / Lipopolysaccharide-assembly, LptC-related / Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / : / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NOVOBIOCIN / Lipopolysaccharide export system permease protein LptG / Lipopolysaccharide export system ATP-binding protein LptB / Lipopolysaccharide export system protein LptC / Lipopolysaccharide export system permease protein LptF / Lipopolysaccharide export system permease protein LptF
Similarity search - Component
Biological speciesEnterobacter cloacae subsp. cloacae (bacteria)
Enterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsOwens, T.W. / Kahne, D. / Kruse, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 GM066174 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI081059 United States
CitationJournal: Nature / Year: 2019
Title: Structural basis of unidirectional export of lipopolysaccharide to the cell surface.
Authors: Owens, T.W. / Taylor, R.J. / Pahil, K.S. / Bertani, B.R. / Ruiz, N. / Kruse, A.C. / Kahne, D.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 21, 2020Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rpim_I_all
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipopolysaccharide export system ATP-binding protein
B: Lipopolysaccharide export system ATP-binding protein
C: Lipopolysaccharide export system protein LptC
F: LPS export ABC transporter permease LptF
G: Lipopolysaccharide export system permease protein LptG
D: Lipopolysaccharide export system ATP-binding protein
E: Lipopolysaccharide export system ATP-binding protein
H: Lipopolysaccharide export system protein LptC
I: LPS export ABC transporter permease LptF
J: Lipopolysaccharide export system permease protein LptG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,79223
Polymers312,08710
Non-polymers1,70513
Water1448
1
A: Lipopolysaccharide export system ATP-binding protein
B: Lipopolysaccharide export system ATP-binding protein
C: Lipopolysaccharide export system protein LptC
F: LPS export ABC transporter permease LptF
G: Lipopolysaccharide export system permease protein LptG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,75113
Polymers156,0435
Non-polymers7088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-195 kcal/mol
Surface area61590 Å2
MethodPISA
2
D: Lipopolysaccharide export system ATP-binding protein
E: Lipopolysaccharide export system ATP-binding protein
H: Lipopolysaccharide export system protein LptC
I: LPS export ABC transporter permease LptF
J: Lipopolysaccharide export system permease protein LptG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,04010
Polymers156,0435
Non-polymers9975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-151 kcal/mol
Surface area61380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.427, 156.984, 295.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Lipopolysaccharide export system ... , 3 types, 8 molecules ABDECHGJ

#1: Protein
Lipopolysaccharide export system ATP-binding protein


Mass: 26819.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_04583 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CR83
#2: Protein Lipopolysaccharide export system protein LptC


Mass: 22255.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: lptC, ECL_04581 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CU18
#4: Protein Lipopolysaccharide export system permease protein LptG


Mass: 39566.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_04592 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CQA2

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Protein , 1 types, 2 molecules FI

#3: Protein LPS export ABC transporter permease LptF / Lipopolysaccharide export system permease protein lptF


Mass: 40582.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: lptF, CP904_11410, ERS370009_01510 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A232G4N0, UniProt: A0A421IFY4*PLUS

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Non-polymers , 4 types, 21 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Chemical ChemComp-NOV / NOVOBIOCIN / 4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside


Mass: 612.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C31H36N2O11 / Comment: antibiotic*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.33 Å3/Da / Density % sol: 71.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 21% PEG 400, 100mM MES pH 6.5, 500mM Li2SO4, 2mM Na-novobiocin

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03324 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 3→49.33 Å / Num. obs: 109124 / % possible obs: 100 % / Redundancy: 16 % / CC1/2: 0.723 / Rmerge(I) obs: 0.48 / Rpim(I) all: 0.13 / Rrim(I) all: 0.499 / Net I/σ(I): 5.6 / Num. measured all: 1745941 / Scaling rejects: 2870
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs% possible allRmerge(I) obsRpim(I) all
3-3.0512.26499153370.13786.5920.299.7
16.43-49.3315.9118067440.9980.0982096.10.0950.024

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.2 Å49.33 Å
Translation3.2 Å49.33 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.1data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5l75

5l75


Resolution: 3.2→49.326 Å / SU ML: 0.8 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 42.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3201 1641 1.83 %
Rwork0.279 87828 -
obs0.2798 89469 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 239.34 Å2 / Biso mean: 136.5073 Å2 / Biso min: 67.8 Å2
Refinement stepCycle: final / Resolution: 3.2→49.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19625 0 100 8 19733
Biso mean--142.68 103.63 -
Num. residues----2657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.29410.5251240.5436718684293
3.2941-3.40040.45341370.423372887425100
3.4004-3.52190.41011360.364772787414100
3.5219-3.66290.3941350.327172637398100
3.6629-3.82960.31511380.300973067444100
3.8296-4.03140.33491370.271473217458100
4.0314-4.28380.30721360.255373177453100
4.2838-4.61440.28681380.236773427480100
4.6144-5.07830.24821370.233873767513100
5.0783-5.81210.34471380.279474157553100
5.8121-7.31890.34351400.307974677607100
7.3189-49.3320.29661450.254777377882100

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