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- PDB-5lj6: Structure of Aggregatibacter actinomycetemcomitans MacB bound to ... -

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Basic information

Entry
Database: PDB / ID: 5lj6
TitleStructure of Aggregatibacter actinomycetemcomitans MacB bound to ATPyS (P6522)
ComponentsMacrolide export ATP-binding/permease protein MacB
KeywordsTRANSPORT PROTEIN / Membrane Protein ABC Transporter
Function / homology
Function and homology information


Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Macrolide export ATP-binding/permease protein macB family profile. / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...Macrolide export ATP-binding/permease protein macB family profile. / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / 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'-TRIPHOSPHATE / Macrolide export ATP-binding/permease protein MacB
Similarity search - Component
Biological speciesAggregatibacter actinomycetemcomitans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsCrow, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N000994/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure and mechanotransmission mechanism of the MacB ABC transporter superfamily.
Authors: Crow, A. / Greene, N.P. / Kaplan, E. / Koronakis, V.
History
DepositionJul 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: 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: Macrolide export ATP-binding/permease protein MacB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6463
Polymers72,1151
Non-polymers5312
Water00
1
A: Macrolide export ATP-binding/permease protein MacB
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)145,2926
Polymers144,2292
Non-polymers1,0634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area8000 Å2
ΔGint-75 kcal/mol
Surface area53380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.570, 119.570, 307.779
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 72114.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria)
Gene: macB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43
References: UniProt: Q2EHL8, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 4.4 Å3/Da / Density % sol: 72.07 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: PEG 400, Sodium Citrate, Magnesium Chloride, ATPyS, Dodecylmaltopyranoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97943 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 3.9→61.56 Å / Num. obs: 21959 / % possible obs: 97.9 % / Redundancy: 13.8 % / Rsym value: 0.103 / Net I/σ(I): 10.3
Reflection shellHighest resolution: 3.9 Å / Rsym value: 2.466

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Processing

Software
NameVersionClassification
PHENIX(dev_2196: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Higher resolution MacB structure in space group P21

Resolution: 3.9→59.785 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 34.9
RfactorNum. reflection% reflection
Rfree0.3222 1195 5.44 %
Rwork0.2675 --
obs0.2699 21959 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.9→59.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4564 0 32 0 4596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044643
X-RAY DIFFRACTIONf_angle_d1.0256262
X-RAY DIFFRACTIONf_dihedral_angle_d16.4822829
X-RAY DIFFRACTIONf_chiral_restr0.052762
X-RAY DIFFRACTIONf_plane_restr0.004786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.05610.41871160.38032237X-RAY DIFFRACTION94
4.0561-4.24070.35851490.34432223X-RAY DIFFRACTION95
4.2407-4.46420.38321240.31032242X-RAY DIFFRACTION95
4.4642-4.74380.3761420.26582281X-RAY DIFFRACTION97
4.7438-5.10990.28761330.24732333X-RAY DIFFRACTION100
5.1099-5.62370.35171640.24022323X-RAY DIFFRACTION100
5.6237-6.43670.34651160.26122391X-RAY DIFFRACTION100
6.4367-8.10630.28081420.23692352X-RAY DIFFRACTION100
8.1063-59.7920.30191090.26552382X-RAY DIFFRACTION99

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