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- PDB-5lj9: Structure of the E. coli MacB ABC domain (C2221) -

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Basic information

Entry
Database: PDB / ID: 5lj9
TitleStructure of the E. coli MacB ABC domain (C2221)
ComponentsMacrolide export ATP-binding/permease protein MacB
KeywordsTRANSPORT PROTEIN / Membrane Protein / ABC Transporter
Function / homology
Function and homology information


polymyxin transport / polymyxin transmembrane transporter activity / MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the plasma membrane / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity / transmembrane transporter activity / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity ...polymyxin transport / polymyxin transmembrane transporter activity / MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the plasma membrane / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity / transmembrane transporter activity / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Macrolide export ATP-binding/permease protein MacB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
C: Macrolide export ATP-binding/permease protein MacB


Theoretical massNumber of molelcules
Total (without water)76,8303
Polymers76,8303
Non-polymers00
Water2,144119
1
A: Macrolide export ATP-binding/permease protein MacB


Theoretical massNumber of molelcules
Total (without water)25,6101
Polymers25,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrolide export ATP-binding/permease protein MacB


Theoretical massNumber of molelcules
Total (without water)25,6101
Polymers25,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Macrolide export ATP-binding/permease protein MacB


Theoretical massNumber of molelcules
Total (without water)25,6101
Polymers25,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.470, 96.210, 262.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 2282 - 228
21BB2 - 2282 - 228
12AA2 - 2282 - 228
22CC2 - 2282 - 228
13BB2 - 2292 - 229
23CC2 - 2292 - 229

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 25610.018 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: macB, ybjZ, b0879, JW0863 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: P75831, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: 2.8 M sodium formate, 100 mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.3→52.54 Å / Num. obs: 31381 / % possible obs: 95.2 % / Redundancy: 6.6 % / Rsym value: 0.077 / Net I/σ(I): 14
Reflection shellRsym value: 0.431

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LJA

5lja


Resolution: 2.3→52.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.484 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.232 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22521 1597 5.1 %RANDOM
Rwork0.18601 ---
obs0.18804 29723 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.977 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--1.42 Å20 Å2
3----0.65 Å2
Refinement stepCycle: 1 / Resolution: 2.3→52.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5318 0 0 119 5437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195542
X-RAY DIFFRACTIONr_bond_other_d0.0070.025415
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9617509
X-RAY DIFFRACTIONr_angle_other_deg1.43312381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75823.321277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95715977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8091561
X-RAY DIFFRACTIONr_chiral_restr0.10.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026450
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021313
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4613.5012807
X-RAY DIFFRACTIONr_mcbond_other3.4433.52806
X-RAY DIFFRACTIONr_mcangle_it5.1235.2313528
X-RAY DIFFRACTIONr_mcangle_other5.1255.2343529
X-RAY DIFFRACTIONr_scbond_it4.994.2662734
X-RAY DIFFRACTIONr_scbond_other4.9894.2672735
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9576.1363981
X-RAY DIFFRACTIONr_long_range_B_refined10.3127.6265822
X-RAY DIFFRACTIONr_long_range_B_other10.31227.6135807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A283620.07
12B283620.07
21A281820.08
22C281820.08
31B283040.1
32C283040.1
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 112 -
Rwork0.222 1860 -
obs--82.68 %

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