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- PDB-4zjq: Crystal structure of AcrB deletion mutant in complex with antibio... -

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Basic information

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


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / 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 TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.592 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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)684,24219
Polymers678,5136
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)342,15010
Polymers339,2573
Non-polymers2,8947
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)342,0929
Polymers339,2573
Non-polymers2,8356
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.055, 154.575, 215.740
Angle α, β, γ (deg.)90.00, 92.42, 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: 113085.523 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / 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: 3.68 Å3/Da / Density % sol: 66.61 %
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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.59→125.83 Å / Num. obs: 114348 / % possible obs: 100 % / Redundancy: 6.1 % / Net I/σ(I): 5.3
Reflection shellResolution: 3.59→3.79 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2 / % 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: 3.592→19.963 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3187 5678 5.01 %
Rwork0.2458 --
obs0.2494 113282 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.592→19.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47312 0 385 0 47697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01448629
X-RAY DIFFRACTIONf_angle_d1.79566044
X-RAY DIFFRACTIONf_dihedral_angle_d16.7317568
X-RAY DIFFRACTIONf_chiral_restr0.0737827
X-RAY DIFFRACTIONf_plane_restr0.0088381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5917-3.63220.40531540.33683002X-RAY DIFFRACTION84
3.6322-3.67470.40851990.32473573X-RAY DIFFRACTION100
3.6747-3.71930.39211880.31213625X-RAY DIFFRACTION100
3.7193-3.7660.39041930.31583564X-RAY DIFFRACTION100
3.766-3.81520.37851740.29843593X-RAY DIFFRACTION100
3.8152-3.86710.35772070.28533600X-RAY DIFFRACTION100
3.8671-3.9220.35331870.27413605X-RAY DIFFRACTION100
3.922-3.98010.31641820.27573594X-RAY DIFFRACTION100
3.9801-4.04180.38552060.27533575X-RAY DIFFRACTION100
4.0418-4.10750.36851830.273601X-RAY DIFFRACTION100
4.1075-4.17770.34171870.2573643X-RAY DIFFRACTION100
4.1777-4.25290.35562000.2583555X-RAY DIFFRACTION100
4.2529-4.33390.32351860.26023623X-RAY DIFFRACTION100
4.3339-4.42140.33871830.26093639X-RAY DIFFRACTION100
4.4214-4.51650.35481930.25833565X-RAY DIFFRACTION100
4.5165-4.62030.32121820.25763617X-RAY DIFFRACTION100
4.6203-4.73430.37752040.2713589X-RAY DIFFRACTION100
4.7343-4.86050.31671870.25573613X-RAY DIFFRACTION100
4.8605-5.00140.33891900.23643635X-RAY DIFFRACTION100
5.0014-5.16010.30581950.24213587X-RAY DIFFRACTION99
5.1601-5.34120.31731910.25533559X-RAY DIFFRACTION100
5.3412-5.55060.34441940.24543642X-RAY DIFFRACTION100
5.5506-5.79730.32681920.24673610X-RAY DIFFRACTION100
5.7973-6.09470.34341930.24543604X-RAY DIFFRACTION100
6.0947-6.46440.34031920.24713643X-RAY DIFFRACTION100
6.4644-6.94390.32081900.23163623X-RAY DIFFRACTION100
6.9439-7.60740.29261860.20573626X-RAY DIFFRACTION100
7.6074-8.62940.24511900.18493678X-RAY DIFFRACTION100
8.6294-10.59450.22531880.18213643X-RAY DIFFRACTION100
10.5945-19.96380.28981820.25253578X-RAY DIFFRACTION96

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