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- PDB-6o30: Lipid A transporter MsbA from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 6o30
TitleLipid A transporter MsbA from Salmonella typhimurium
ComponentsLipid A export ATP-binding/permease protein MsbA
KeywordsMEMBRANE PROTEIN / MSBA / LIPID A CO-CRYSTALLIZATION / ABC TRANSPORTERS / STAPHYLOCOCCUS TYPHIMURIUM
Function / homology
Function and homology information


ABC-type lipid A-core oligosaccharide transporter / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Lipid A export ATP-binding/permease protein msbA family profile. / 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 ...Lipid A export ATP-binding/permease protein msbA family profile. / 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
ATP-dependent lipid A-core flippase / ATP-dependent lipid A-core flippase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.47 Å
AuthorsPadayatti, P.S. / Zhang, Q. / Wilson, I.A. / Lee, S.C. / Stanfield, R.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM09853 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM118594 United States
CitationJournal: Structure / Year: 2019
Title: Structural Insights into the Lipid A Transport Pathway in MsbA.
Authors: Padayatti, P.S. / Lee, S.C. / Stanfield, R.L. / Wen, P.C. / Tajkhorshid, E. / Wilson, I.A. / Zhang, Q.
History
DepositionFeb 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 4, 2020Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all
Revision 1.4Oct 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

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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


Theoretical massNumber of molelcules
Total (without water)127,3312
Polymers127,3312
Non-polymers00
Water0
1
A: Lipid A export ATP-binding/permease protein MsbA

A: Lipid A export ATP-binding/permease protein MsbA


Theoretical massNumber of molelcules
Total (without water)127,3312
Polymers127,3312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area10110 Å2
ΔGint-97 kcal/mol
Surface area54220 Å2
MethodPISA
2
B: Lipid A export ATP-binding/permease protein MsbA

B: Lipid A export ATP-binding/permease protein MsbA


Theoretical massNumber of molelcules
Total (without water)127,3312
Polymers127,3312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10480 Å2
ΔGint-101 kcal/mol
Surface area53960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.257, 153.200, 232.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 63665.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: msbA, DD95_15660, EIL76_15590 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K6RU95, UniProt: P63359*PLUS, ABC-type lipid A-core oligosaccharide transporter

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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: 5.76 Å3/Da / Density % sol: 78.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MSBA PURIFIED IN DETERGENT MICELLES (UDM/FA231) IS MIXED 1: 1 WITH WELL SOLUTION (20 MM TRIS-HCL (PH 7.5) AND 27.5% PEG 300).

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 4.47→46.8 Å / Num. obs: 15470 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 194 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.077 / Rrim(I) all: 0.138 / Net I/σ(I): 10
Reflection shellResolution: 4.47→4.81 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.66 / Num. unique obs: 683 / Rpim(I) all: 1.11 / Rrim(I) all: 2.01 / % possible all: 75.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BL6

6bl6


Resolution: 4.47→46.754 Å / SU ML: 0.89 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 52.61
RfactorNum. reflection% reflection
Rfree0.3395 719 4.8 %
Rwork0.3068 --
obs0.3083 14965 80.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.47→46.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8894 0 0 0 8894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039028
X-RAY DIFFRACTIONf_angle_d0.77912202
X-RAY DIFFRACTIONf_dihedral_angle_d13.1685484
X-RAY DIFFRACTIONf_chiral_restr0.0481452
X-RAY DIFFRACTIONf_plane_restr0.0081542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.465-4.80940.44221110.39862190X-RAY DIFFRACTION63
4.8094-5.29280.41211240.37562700X-RAY DIFFRACTION78
5.2928-6.05730.43511370.3962741X-RAY DIFFRACTION78
6.0573-7.62620.39421640.34953223X-RAY DIFFRACTION91
7.6262-46.75640.29851830.27253392X-RAY DIFFRACTION92

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