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

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Basic information

Entry
Database: PDB / ID: 5lil
TitleStructure of Aggregatibacter actinomycetemcomitans MacB bound to ATPyS (P21)
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 / 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 family / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...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 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
ADENOSINE-5'-TRIPHOSPHATE / Macrolide export ATP-binding/permease protein MacB
Similarity search - Component
Biological speciesAggregatibacter actinomycetemcomitans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.35 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 15, 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 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)145,2926
Polymers144,2292
Non-polymers1,0634
Water724
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-73 kcal/mol
Surface area53130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.587, 82.621, 124.920
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 72114.703 Da / Num. of mol.: 2 / Mutation: E169Q
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): C43(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 / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 3.98 Å3/Da / Density % sol: 69.1 %
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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.35→79.95 Å / Num. obs: 63156 / % possible obs: 99.6 % / Redundancy: 9.3 % / Rsym value: 0.284 / Net I/σ(I): 7.7
Reflection shellRsym value: 1.522

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Processing

Software
NameVersionClassification
PHENIX(dev_2196: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 3.35→79.946 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.4
RfactorNum. reflection% reflection
Rfree0.2902 3074 4.87 %
Rwork0.2444 --
obs0.2466 63156 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.35→79.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9255 0 64 4 9323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039414
X-RAY DIFFRACTIONf_angle_d0.71112698
X-RAY DIFFRACTIONf_dihedral_angle_d14.8885743
X-RAY DIFFRACTIONf_chiral_restr0.0441543
X-RAY DIFFRACTIONf_plane_restr0.0031598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3503-3.40260.34241360.37112602X-RAY DIFFRACTION93
3.4026-3.45840.37361040.35092665X-RAY DIFFRACTION97
3.4584-3.5180.3612910.32912732X-RAY DIFFRACTION98
3.518-3.5820.37551140.32422772X-RAY DIFFRACTION98
3.582-3.65090.33951500.29492723X-RAY DIFFRACTION98
3.6509-3.72540.28031450.28342701X-RAY DIFFRACTION98
3.7254-3.80640.34341530.27412675X-RAY DIFFRACTION99
3.8064-3.8950.32471760.25882714X-RAY DIFFRACTION99
3.895-3.99240.29491500.24792740X-RAY DIFFRACTION99
3.9924-4.10030.32791480.24552727X-RAY DIFFRACTION99
4.1003-4.2210.2941340.23222754X-RAY DIFFRACTION100
4.221-4.35720.2796950.21832806X-RAY DIFFRACTION99
4.3572-4.51290.26651150.20372753X-RAY DIFFRACTION100
4.5129-4.69360.25231770.19192720X-RAY DIFFRACTION99
4.6936-4.90720.27731500.19492751X-RAY DIFFRACTION100
4.9072-5.16590.2571560.20262760X-RAY DIFFRACTION99
5.1659-5.48940.25881180.21752761X-RAY DIFFRACTION100
5.4894-5.91320.28751370.23852757X-RAY DIFFRACTION99
5.9132-6.5080.31891300.24722747X-RAY DIFFRACTION100
6.508-7.44910.26221600.22932773X-RAY DIFFRACTION100
7.4491-9.38280.21791710.19112714X-RAY DIFFRACTION100
9.3828-79.96920.30881640.27162735X-RAY DIFFRACTION100

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