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- PDB-3b5z: Crystal Structure of MsbA from Salmonella typhimurium with ADP Va... -

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Basic information

Entry
Database: PDB / ID: 3b5z
TitleCrystal Structure of MsbA from Salmonella typhimurium with ADP Vanadate
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


ABC-type lipid A-core oligosaccharide transporter / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / 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
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / ATP-dependent lipid A-core flippase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.2 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 1.2May 29, 2013Group: Non-polymer description
Revision 1.3Jun 5, 2013Group: Derived calculations / Non-polymer description
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,80212
Polymers257,6344
Non-polymers2,1698
Water00
1
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)129,9016
Polymers128,8172
Non-polymers1,0844
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,9016
Polymers128,8172
Non-polymers1,0844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)267.169, 121.103, 176.744
Angle α, β, γ (deg.)90.00, 121.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 64408.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: msbA / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): bl21
References: UniProt: P63359, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: VO4

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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: 4.73 Å3/Da / Density % sol: 73.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 100mM NaCl, 325mM NaCH3COO, 19% PEG 400, 15mM ATP, 20mM MgCl2, 1mM sodium ortho-vanadate and 0.05% beta-UDM, pH 7.7, VAPOR DIFFUSION, SITTING DROP, 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: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.2→20 Å / Num. all: 30164 / Num. obs: 30164 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.088
Reflection shellResolution: 4.2→4.46 Å / Num. unique all: 3907 / % possible all: 73.6

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 4.2→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 5020364.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.362 2123 7 %RANDOM
Rwork0.336 ---
obs-30164 86.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.87 Å2 / ksol: 0.15 e/Å3
Displacement parametersBiso mean: 155.7 Å2
Baniso -1Baniso -2Baniso -3
1-22.33 Å20 Å213.23 Å2
2---14.94 Å20 Å2
3----7.39 Å2
Refinement stepCycle: LAST / Resolution: 4.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 112 0 2400
LS refinement shellResolution: 4.2→4.46 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.532 324 7.7 %
Rwork0.509 3907 -
all-4231 -
obs--73.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2atp.par

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