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- PDB-3b5w: Crystal Structure of Eschericia coli MsbA -

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Basic information

Entry
Database: PDB / ID: 3b5w
TitleCrystal Structure of Eschericia coli MsbA
ComponentsLipid A export ATP-binding/permease protein msbA
KeywordsMEMBRANE PROTEIN / ABC transporter / MsbA / lipid flippase / ATP-binding / Hydrolase / Inner membrane / Lipid transport / Membrane / Nucleotide-binding / Transmembrane
Function / homology
Function and homology information


MsbA transporter complex / lipopolysaccharide floppase activity / lipid translocation / ABC-type lipid A-core oligosaccharide transporter / lipopolysaccharide transport / ATPase-coupled lipid transmembrane transporter activity / ABC-type xenobiotic transporter activity / lipid transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport ...MsbA transporter complex / lipopolysaccharide floppase activity / lipid translocation / ABC-type lipid A-core oligosaccharide transporter / lipopolysaccharide transport / ATPase-coupled lipid transmembrane transporter activity / ABC-type xenobiotic transporter activity / lipid transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / lipid binding / ATP hydrolysis activity / ATP binding / membrane / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 5.3 Å
AuthorsWard, A. / Reyes, C.L. / Yu, J. / Roth, C.B. / Chang, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Flexibility in the ABC transporter MsbA: Alternating access with a twist.
Authors: Ward, A. / Reyes, C.L. / Yu, J. / Roth, C.B. / Chang, G.
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Lipid A export ATP-binding/permease protein msbA
D: Lipid A export ATP-binding/permease protein msbA
E: Lipid A export ATP-binding/permease protein msbA
F: Lipid A export ATP-binding/permease protein msbA
G: Lipid A export ATP-binding/permease protein msbA
H: Lipid A export ATP-binding/permease protein msbA


Theoretical massNumber of molelcules
Total (without water)516,2448
Polymers516,2448
Non-polymers00
Water0
1
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)129,0612
Polymers129,0612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lipid A export ATP-binding/permease protein msbA
D: Lipid A export ATP-binding/permease protein msbA


Theoretical massNumber of molelcules
Total (without water)129,0612
Polymers129,0612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Lipid A export ATP-binding/permease protein msbA
F: Lipid A export ATP-binding/permease protein msbA


Theoretical massNumber of molelcules
Total (without water)129,0612
Polymers129,0612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Lipid A export ATP-binding/permease protein msbA
H: Lipid A export ATP-binding/permease protein msbA


Theoretical massNumber of molelcules
Total (without water)129,0612
Polymers129,0612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.790, 126.070, 206.560
Angle α, β, γ (deg.)83.470, 76.250, 84.070
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Lipid A export ATP-binding/permease protein msbA / Coordinate model: Cα atoms only


Mass: 64530.543 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: msbA / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P60752, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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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: 5.23 Å3/Da / Density % sol: 76.5 %
Crystal growTemperature: 277 K / Method: sitting drop vapor diffusion / pH: 7.5
Details: 15-20% PEG 300, 80-120mM LiSO4 and 0.05% alpha-DDM., pH 7.5, sitting drop vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 5.3→20 Å / Num. all: 36078 / Num. obs: 36078 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.046

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementResolution: 5.3→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 387600.344 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: This entry contains C-alpha atoms only; BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.311 3675 10.2 %RANDOM
Rwork0.276 ---
obs-36078 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 194.2 Å2 / ksol: 0.15 e/Å3
Displacement parametersBiso mean: 308.7 Å2
Baniso -1Baniso -2Baniso -3
1--20.35 Å2-67.08 Å234.83 Å2
2--27.14 Å2-9.9 Å2
3----6.79 Å2
Refinement stepCycle: LAST / Resolution: 5.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4576 0 0 0 4576
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2

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