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- PDB-5ws4: Crystal structure of tripartite-type ABC transporter MacB from Ac... -

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Basic information

Entry
Database: PDB / ID: 5ws4
TitleCrystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii
ComponentsMacrolide export ATP-binding/permease protein MacB
KeywordsMEMBRANE PROTEIN / Multi-drug efflux transporter / ABC transporter / Drug exporter
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease family / 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. ...MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease family / 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-AT4 / ABC transporter family protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsMurakami, S. / Okada, U. / Yamashita, E.
Funding support Japan, 4items
OrganizationGrant numberCountry
MEXT Japan
JSPS Japan
JST Japan
NIBIO Japan
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii.
Authors: Okada, U. / Yamashita, E. / Neuberger, A. / Morimoto, M. / van Veen, H.W. / Murakami, S.
History
DepositionDec 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Macrolide export ATP-binding/permease protein MacB
B: Macrolide export ATP-binding/permease protein MacB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4314
Polymers144,5452
Non-polymers8872
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-35 kcal/mol
Surface area56970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.652, 229.652, 154.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Macrolide export ATP-binding/permease protein MacB


Mass: 72272.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: macB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0D8G707, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-AT4 / 5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE / ADENOSINE 5'-O-(2-THIODIPHOSPHATE)


Mass: 443.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O9P2S

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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: 7.05 Å3/Da / Density % sol: 82.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 1.2M Sodium citric acid, 0.1M Sodium HEPES (pH7.2)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.75 Å
DetectorType: MAR scanner 300 mm plate / Detector: CCD / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 46498 / % possible obs: 99.9 % / Redundancy: 16.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 27.5
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 15.8 % / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.4→49.115 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 0.08 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2357 5.06 %
Rwork0.227 --
obs0.2285 46498 81.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→49.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9770 0 54 0 9824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049948
X-RAY DIFFRACTIONf_angle_d0.81913496
X-RAY DIFFRACTIONf_dihedral_angle_d2.6136012
X-RAY DIFFRACTIONf_chiral_restr0.0491632
X-RAY DIFFRACTIONf_plane_restr0.0051746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.43860.1707100.2923488X-RAY DIFFRACTION14
3.4386-3.47910.332390.2805899X-RAY DIFFRACTION26
3.4791-3.52150.3590.26761230X-RAY DIFFRACTION36
3.5215-3.56610.3457610.2821413X-RAY DIFFRACTION41
3.5661-3.6130.3155960.26181617X-RAY DIFFRACTION47
3.613-3.66250.3431900.25841844X-RAY DIFFRACTION54
3.6625-3.71480.2742980.25342070X-RAY DIFFRACTION60
3.7148-3.77020.25271190.2562237X-RAY DIFFRACTION65
3.7702-3.82910.29141470.25352450X-RAY DIFFRACTION71
3.8291-3.89180.28451390.25892590X-RAY DIFFRACTION76
3.8918-3.95890.27911950.25872749X-RAY DIFFRACTION81
3.9589-4.03090.23251440.24482980X-RAY DIFFRACTION87
4.0309-4.10840.24921670.22883152X-RAY DIFFRACTION92
4.1084-4.19220.25511690.22383351X-RAY DIFFRACTION97
4.1922-4.28330.24532020.21993385X-RAY DIFFRACTION100
4.2833-4.38290.28051600.21513441X-RAY DIFFRACTION100
4.3829-4.49240.23381960.23419X-RAY DIFFRACTION100
4.4924-4.61380.23182050.19643433X-RAY DIFFRACTION100
4.6138-4.74940.24061840.18233408X-RAY DIFFRACTION100
4.7494-4.90260.21851460.18653445X-RAY DIFFRACTION100
4.9026-5.07760.25541970.21393429X-RAY DIFFRACTION100
5.0776-5.28070.27751610.20853439X-RAY DIFFRACTION100
5.2807-5.52070.24911710.22633468X-RAY DIFFRACTION100
5.5207-5.81140.25351700.23213423X-RAY DIFFRACTION100
5.8114-6.17480.28671940.24223416X-RAY DIFFRACTION100
6.1748-6.65050.26011960.23883416X-RAY DIFFRACTION100
6.6505-7.31780.25722200.22823400X-RAY DIFFRACTION100
7.3178-8.37220.23622070.21163414X-RAY DIFFRACTION100
8.3722-10.5310.18911860.17333418X-RAY DIFFRACTION100
10.531-49.11980.31651380.28483342X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 66.3132 Å / Origin y: 66.489 Å / Origin z: 44.3118 Å
111213212223313233
T0.0341 Å2-0.3305 Å20.0755 Å2-0.1253 Å20.0192 Å2--0.103 Å2
L0.0876 °2-0.0579 °2-0.0676 °2-0.0863 °2-0.0354 °2---0.011 °2
S0.0734 Å °-0.0061 Å °0.0244 Å °-0.1569 Å °-0.0236 Å °-0.0206 Å °0.0237 Å °-0.0756 Å °0.0525 Å °
Refinement TLS groupSelection details: all

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