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- PDB-5lj7: Structure of Aggregatibacter actinomycetemcomitans MacB bound to ... -

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Basic information

Entry
Database: PDB / ID: 5lj7
TitleStructure of Aggregatibacter actinomycetemcomitans MacB bound to ATP (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 / 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 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 / MOLECULAR REPLACEMENT / Resolution: 3.25 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 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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 author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-76 kcal/mol
Surface area52360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.328, 82.610, 125.170
Angle α, β, γ (deg.)90.00, 93.54, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria)
Gene: macB / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 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


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: 4.23 Å3/Da / Density % sol: 70.93 %
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: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.25→86.13 Å / Num. obs: 70100 / % possible obs: 99.4 % / Redundancy: 6.1 % / Rsym value: 0.21 / Net I/σ(I): 6.7
Reflection shellHighest resolution: 3.25 Å / Rsym value: 1.317

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Processing

Software
NameVersionClassification
PHENIX(dev_2196: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LIL

5lil


Resolution: 3.25→86.126 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 36.35
RfactorNum. reflection% reflection
Rfree0.2994 3407 4.86 %
Rwork0.2462 --
obs0.2488 70100 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.25→86.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9058 0 64 4 9126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039211
X-RAY DIFFRACTIONf_angle_d0.57712419
X-RAY DIFFRACTIONf_dihedral_angle_d13.7295620
X-RAY DIFFRACTIONf_chiral_restr0.0411510
X-RAY DIFFRACTIONf_plane_restr0.0021561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.29640.36571450.34412834X-RAY DIFFRACTION100
3.2964-3.34560.44241550.32572701X-RAY DIFFRACTION99
3.3456-3.39790.35241440.3292834X-RAY DIFFRACTION99
3.3979-3.45360.35581180.29612806X-RAY DIFFRACTION99
3.4536-3.51320.4197900.28452828X-RAY DIFFRACTION99
3.5132-3.57710.32121350.27222826X-RAY DIFFRACTION99
3.5771-3.64590.2741240.25762732X-RAY DIFFRACTION100
3.6459-3.72030.29961440.25952759X-RAY DIFFRACTION99
3.7203-3.80120.29141810.24622821X-RAY DIFFRACTION99
3.8012-3.88960.35591810.24122724X-RAY DIFFRACTION100
3.8896-3.98690.25451380.23832811X-RAY DIFFRACTION99
3.9869-4.09470.33611550.23812730X-RAY DIFFRACTION99
4.0947-4.21520.291370.23522741X-RAY DIFFRACTION99
4.2152-4.35120.29341100.21982913X-RAY DIFFRACTION99
4.3512-4.50670.31721010.21072761X-RAY DIFFRACTION99
4.5067-4.68720.25641620.21012686X-RAY DIFFRACTION95
4.6872-4.90050.2871420.20552718X-RAY DIFFRACTION99
4.9005-5.15880.26281660.21632812X-RAY DIFFRACTION99
5.1588-5.4820.27851100.22972798X-RAY DIFFRACTION99
5.482-5.90510.27341380.24512803X-RAY DIFFRACTION100
5.9051-6.49920.30221390.2622806X-RAY DIFFRACTION100
6.4992-7.43920.29151560.2452781X-RAY DIFFRACTION100
7.4392-9.37080.22271760.21132769X-RAY DIFFRACTION100
9.3708-86.15660.32831600.27522699X-RAY DIFFRACTION97

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