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- PDB-6bpl: E. coli MsbA in complex with LPS and inhibitor G907 -

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Basic information

Entry
Database: PDB / ID: 6bpl
TitleE. coli MsbA in complex with LPS and inhibitor G907
ComponentsLipid A export ATP-binding/permease protein MsbA
KeywordsLIPID TRANSPORT / ABC transporter / inhibitor / LPS / MsbA
Function / homology
Function and homology information


ABC-type lipid A-core oligosaccharide transporter / ATPase-coupled lipid transmembrane transporter activity / ATPase activity / integral component of membrane / ATP binding / identical protein binding / plasma membrane
ABC transporter, conserved site / Type I protein exporter / Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter integral membrane type-1 fused domain profile. / ATP-binding cassette, ABC transporter-type domain profile. / ABC transporters family signature. / ABC transporter transmembrane region / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain ...ABC transporter, conserved site / Type I protein exporter / Lipid A export ATP-binding/permease protein msbA family profile. / ABC transporter integral membrane type-1 fused domain profile. / ATP-binding cassette, ABC transporter-type domain profile. / ABC transporters family signature. / ABC transporter transmembrane region / ABC transporter-like / AAA+ ATPase domain / ABC transporter type 1, transmembrane domain / ABC transporter, lipid A export, MsbA / ABC transporter / P-loop containing nucleoside triphosphate hydrolase / ABC transporter type 1, transmembrane domain superfamily
Lipid A export ATP-binding/permease protein MsbA / Lipid A export ATP-binding/permease protein MsbA
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.908 Å
AuthorsHo, H. / Koth, C.M. / Payandeh, J.
CitationJournal: Nature / Year: 2018
Title: Structural basis for dual-mode inhibition of the ABC transporter MsbA.
Authors: Ho, H. / Miu, A. / Alexander, M.K. / Garcia, N.K. / Oh, A. / Zilberleyb, I. / Reichelt, M. / Austin, C.D. / Tam, C. / Shriver, S. / Hu, H. / Labadie, S.S. / Liang, J. / Wang, L. / Wang, J. / Lu, Y. / Purkey, H.E. / Quinn, J. / Franke, Y. / Clark, K. / Beresini, M.H. / Tan, M.W. / Sellers, B.D. / Maurer, T. / Koehler, M.F.T. / Wecksler, A.T. / Kiefer, J.R. / Verma, V. / Xu, Y. / Nishiyama, M. / Payandeh, J. / Koth, C.M.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 12, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipid A export ATP-binding/permease protein MsbA
B: Lipid A export ATP-binding/permease protein MsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,60927
Polymers128,9732
Non-polymers7,63625
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20900 Å2
ΔGint-50 kcal/mol
Surface area51030 Å2
Unit cell
γ
α
β
Length a, b, c (Å)74.747, 91.606, 111.013
Angle α, β, γ (deg.)90.00, 89.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide Lipid A export ATP-binding/permease protein MsbA


Mass: 64486.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria)
Strain: CFT073 / ATCC 700928 / UPEC / Gene: msbA, c1054 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q8FJB1, UniProt: P60753*PLUS, Hydrolases, Acting on acid anhydrides, Acting on acid anhydrides to catalyse transmembrane movement of substances

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Non-polymers , 12 types, 25 molecules

#2: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid *YM
#3: Chemical ChemComp-AU7 / (2E)-3-{6-[(1S)-1-(2-chloro-6-cyclopropylphenyl)ethoxy]-4-cyclopropylquinolin-3-yl}prop-2-enoic acid


Mass: 433.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24ClNO3
#4: Chemical
ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O3
#5: Chemical ChemComp-GMH / L-GLYCERO-D-MANNO-HEPTOPYRANOSE


Mass: 210.182 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C7H14O7
#6: Chemical ChemComp-GLC / ALPHA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Glucose
#7: Chemical ChemComp-PA1 / 2-amino-2-deoxy-alpha-D-glucopyranose


Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Phosphate
#9: Chemical ChemComp-GCS / D-GLUCOSAMINE / 2-AMINO-2-DEOXY-D-GLUCOSE


Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5 / Glucosamine
#10: Chemical ChemComp-KDO / 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID


Mass: 238.192 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H14O8 / 3-Deoxy-D-manno-oct-2-ulosonic acid
#11: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2 / Lauric acid
#12: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Myristic acid
#13: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2 / Pyrophosphate

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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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 mM NaCl, 19% PEG 550 MME, 4% PEG 400, 100 mM HEPES, pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9079→39.9 Å / Num. obs: 29686 / % possible obs: 91.1 % / Redundancy: 4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.97
Reflection shellResolution: 2.9079→3.0017 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.53 / Num. unique obs: 1528 / CC1/2: 0.576 / % possible all: 61

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.908→39.9 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.42
RfactorNum. reflection% reflection
Rfree0.2829 1482 4.99 %
Rwork0.2333 --
Obs0.2357 29686 89.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.908→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8827 0 353 0 9180
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0039320
f_angle_d0.66612560
f_dihedral_angle_d17.6565638
f_chiral_restr0.0411507
f_plane_restr0.0031544
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9079-3.00170.4328900.3377143851
3.0017-3.1090.34111220.2927223379
3.109-3.23340.31391300.2707254890
3.2334-3.38050.32181330.2583265893
3.3805-3.55860.29951330.2528257291
3.5586-3.78140.32681450.2322279298
3.7814-4.07310.2751460.2172281198
4.0731-4.48250.24571590.1992271896
4.4825-5.130.22441010.1953283697
5.13-6.45880.30931610.2728279898
6.4588-39.91010.26361620.2283280096

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