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- PDB-7sel: E. coli MsbA in complex with LPS and inhibitor G7090 (compound 3) -

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Basic information

Entry
Database: PDB / ID: 7sel
TitleE. coli MsbA in complex with LPS and inhibitor G7090 (compound 3)
ComponentsATP-dependent lipid A-core flippase
KeywordsTRANSLOCASE / MsbA / Lipid A / LPS / inhibitor / LIPID TRANSPORT
Function / homology
Function and homology information


ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, lipid A-core flippase, MsbA / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...ABC transporter, lipid A-core flippase, MsbA / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-95X / Chem-KDL / Lipid A ABC exporter, fused ATPase and inner membrane subunits MsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.978 Å
AuthorsPayandeh, J. / Koth, C.M. / Verma, V.A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of Inhibitors of the Lipopolysaccharide Transporter MsbA: From a Screening Hit to Potent Wild-Type Gram-Negative Activity.
Authors: Verma, V.A. / Wang, L. / Labadie, S.S. / Liang, J. / Sellers, B.D. / Wang, J. / Dong, L. / Wang, Q. / Zhang, S. / Xu, Z. / Zhang, Y. / Niu, Y. / Wang, X. / Wai, J. / Koehler, M.F.T. / Hu, H. ...Authors: Verma, V.A. / Wang, L. / Labadie, S.S. / Liang, J. / Sellers, B.D. / Wang, J. / Dong, L. / Wang, Q. / Zhang, S. / Xu, Z. / Zhang, Y. / Niu, Y. / Wang, X. / Wai, J. / Koehler, M.F.T. / Hu, H. / Alexander, M.K. / Nishiyama, M. / Miu, A. / Xu, Y. / Pang, J. / Katakam, A.K. / Reichelt, M. / Austin, C.D. / Ho, H. / Payandeh, J. / Koth, C.M.
History
DepositionSep 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent lipid A-core flippase
B: ATP-dependent lipid A-core flippase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,1245
Polymers133,0472
Non-polymers3,0773
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11980 Å2
ΔGint-94 kcal/mol
Surface area52130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.446, 91.990, 110.655
Angle α, β, γ (deg.)90.00, 90.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent lipid A-core flippase / Lipid A export ATP-binding/permease protein MsbA


Mass: 66523.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: msbA, ECBD_2681 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A140NBS6, ABC-type lipid A-core oligosaccharide transporter
#2: Chemical ChemComp-95X / (2E)-3-{7-[(1S)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-1-methylnaphthalen-2-yl}prop-2-enoic acid


Mass: 419.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H17Cl2FO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-KDL / (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid


Mass: 2238.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C110H202N2O39P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: 200 MM NACL, 19% PEG 550 MME, 4% PEG400, 100 MM HEPES, PH7.0, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.978→31.989 Å / Num. obs: 25433 / % possible obs: 94.3 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rpim(I) all: 0.04 / Net I/σ(I): 10.8
Reflection shellResolution: 2.98→3.08 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1092 / CC1/2: 0.7 / Rpim(I) all: 0.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
autoPROCdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 2.978→31.989 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2898 1260 4.95 %
Rwork0.2564 --
obs0.2581 25433 82.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.978→31.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8823 0 144 0 8967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049101
X-RAY DIFFRACTIONf_angle_d0.77312316
X-RAY DIFFRACTIONf_dihedral_angle_d16.9975493
X-RAY DIFFRACTIONf_chiral_restr0.0641471
X-RAY DIFFRACTIONf_plane_restr0.0041542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.978-3.09710.3861720.33021020X-RAY DIFFRACTION32
3.0971-3.23790.3651900.33031547X-RAY DIFFRACTION48
3.2379-3.40840.31841040.30782298X-RAY DIFFRACTION71
3.4084-3.62170.31551740.29183035X-RAY DIFFRACTION95
3.6217-3.90090.33571400.27193259X-RAY DIFFRACTION100
3.9009-4.29260.291610.24193237X-RAY DIFFRACTION100
4.2926-4.91180.25691940.22783218X-RAY DIFFRACTION100
4.9118-6.1810.2661410.26853284X-RAY DIFFRACTION99
6.181-31.9890.27971840.23473275X-RAY DIFFRACTION99

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