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- PDB-4zjo: Crystal structure of AcrB triple mutant in complex with antibioti... -

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Basic information

Entry
Database: PDB / ID: 4zjo
TitleCrystal structure of AcrB triple mutant in complex with antibiotic in P21 space group
ComponentsMultidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport ...alkane transmembrane transporter activity / alkane transport / enterobactin transport / enterobactin transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / periplasmic side of plasma membrane / efflux pump complex / bile acid transmembrane transporter activity / xenobiotic transport / bile acid and bile salt transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / fatty acid transport / response to toxic substance / response to xenobiotic stimulus / response to antibiotic / identical protein binding / membrane / plasma membrane
Similarity search - Function
Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ERYTHROMYCIN A / NICKEL (II) ION / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsAbabou, A. / Koronakis, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Plos One / Year: 2016
Title: Structures of Gate Loop Variants of the AcrB Drug Efflux Pump Bound by Erythromycin Substrate.
Authors: Ababou, A. / Koronakis, V.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value
Revision 1.2Jan 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug efflux pump subunit AcrB
B: Multidrug efflux pump subunit AcrB
C: Multidrug efflux pump subunit AcrB
D: Multidrug efflux pump subunit AcrB
E: Multidrug efflux pump subunit AcrB
F: Multidrug efflux pump subunit AcrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)686,29019
Polymers680,5616
Non-polymers5,72913
Water00
1
A: Multidrug efflux pump subunit AcrB
B: Multidrug efflux pump subunit AcrB
C: Multidrug efflux pump subunit AcrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,17410
Polymers340,2813
Non-polymers2,8947
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22970 Å2
ΔGint-89 kcal/mol
Surface area119300 Å2
MethodPISA
2
D: Multidrug efflux pump subunit AcrB
E: Multidrug efflux pump subunit AcrB
F: Multidrug efflux pump subunit AcrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,1169
Polymers340,2813
Non-polymers2,8356
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22790 Å2
ΔGint-84 kcal/mol
Surface area119740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.184, 156.769, 218.168
Angle α, β, γ (deg.)90.00, 93.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 113426.883 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224
#2: Chemical ChemComp-ERY / ERYTHROMYCIN A


Mass: 733.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H67NO13 / Comment: antibiotic*YM
#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 0.2 M MgAc, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.6→108.89 Å / Num. obs: 117756 / % possible obs: 100 % / Redundancy: 8.7 % / Net I/σ(I): 7.3
Reflection shellResolution: 3.6→3.79 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GIF

2gif


Resolution: 3.6→19.957 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3067 5825 4.99 %
Rwork0.2378 --
obs0.2414 116818 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→19.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47491 0 385 0 47876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01348813
X-RAY DIFFRACTIONf_angle_d1.74766296
X-RAY DIFFRACTIONf_dihedral_angle_d15.5517609
X-RAY DIFFRACTIONf_chiral_restr0.0717859
X-RAY DIFFRACTIONf_plane_restr0.0088417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5995-3.64020.40471740.32583540X-RAY DIFFRACTION96
3.6402-3.68270.41341950.31313672X-RAY DIFFRACTION100
3.6827-3.72740.36811960.29833707X-RAY DIFFRACTION100
3.7274-3.77420.34541840.28843704X-RAY DIFFRACTION100
3.7742-3.82350.35742120.28133697X-RAY DIFFRACTION100
3.8235-3.87560.34792010.28153654X-RAY DIFFRACTION100
3.8756-3.93050.36231940.27223673X-RAY DIFFRACTION100
3.9305-3.98870.34961820.28893723X-RAY DIFFRACTION100
3.9887-4.05050.37212080.28163661X-RAY DIFFRACTION100
4.0505-4.11640.311870.27173735X-RAY DIFFRACTION100
4.1164-4.18670.3481930.26773707X-RAY DIFFRACTION100
4.1867-4.26210.31711920.25763685X-RAY DIFFRACTION100
4.2621-4.34330.31612070.25783689X-RAY DIFFRACTION100
4.3433-4.4310.32131920.24383685X-RAY DIFFRACTION100
4.431-4.52630.30412000.24963697X-RAY DIFFRACTION100
4.5263-4.63030.31981860.25013714X-RAY DIFFRACTION100
4.6303-4.74460.31862050.24423712X-RAY DIFFRACTION100
4.7446-4.8710.32421820.24153680X-RAY DIFFRACTION100
4.871-5.01220.32181960.23733697X-RAY DIFFRACTION100
5.0122-5.17120.33791920.24383722X-RAY DIFFRACTION100
5.1712-5.35260.31011960.253706X-RAY DIFFRACTION100
5.3526-5.56250.36521930.24493699X-RAY DIFFRACTION100
5.5625-5.80970.29861950.23773739X-RAY DIFFRACTION100
5.8097-6.10770.31342030.22883683X-RAY DIFFRACTION100
6.1077-6.4780.30451960.22563731X-RAY DIFFRACTION100
6.478-6.95840.30251970.21273731X-RAY DIFFRACTION100
6.9584-7.6230.27421930.18893738X-RAY DIFFRACTION100
7.623-8.64660.21621860.16433750X-RAY DIFFRACTION100
8.6466-10.61370.17781910.16613740X-RAY DIFFRACTION99
10.6137-19.95690.31961970.24443722X-RAY DIFFRACTION98

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