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- PDB-4ziv: Crystal structure of AcrB triple mutant in P21 space group -

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Basic information

Entry
Database: PDB / ID: 4ziv
TitleCrystal structure of AcrB triple mutant in P21 space group
ComponentsMultidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / AcrB RND efflux pump / Bacterial multidrug resistance / Export mechanism
Function / homology
Function and homology information


alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic transport ...alkane transmembrane transporter activity / alkane transport / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / enterobactin transport / enterobactin transmembrane transporter activity / periplasmic side of plasma membrane / bile acid transmembrane transporter activity / bile acid and bile salt transport / xenobiotic 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 / 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 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 / 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
NICKEL (II) ION / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 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 28, 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)683,80115
Polymers680,5616
Non-polymers3,2409
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)341,9308
Polymers340,2813
Non-polymers1,6495
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)341,8717
Polymers340,2813
Non-polymers1,5914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.278, 157.491, 219.155
Angle α, β, γ (deg.)90.00, 92.74, 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 K-12 (bacteria) / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: 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: 3.86 Å3/Da / Density % sol: 68.11 %
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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.16→109.75 Å / Num. obs: 176847 / % possible obs: 100 % / Redundancy: 17.7 % / Net I/σ(I): 10.2
Reflection shellResolution: 3.16→3.33 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 2.2 / % 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: 3.16→19.979 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3354 8759 4.98 %
Rwork0.27 --
obs0.2732 175873 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.16→19.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47523 0 213 0 47736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01448659
X-RAY DIFFRACTIONf_angle_d1.80166079
X-RAY DIFFRACTIONf_dihedral_angle_d17.30317587
X-RAY DIFFRACTIONf_chiral_restr0.0747809
X-RAY DIFFRACTIONf_plane_restr0.0088421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1595-3.19530.40452910.34855447X-RAY DIFFRACTION98
3.1953-3.23270.42262900.34935570X-RAY DIFFRACTION100
3.2327-3.2720.40322970.34665595X-RAY DIFFRACTION100
3.272-3.31320.42922750.33845543X-RAY DIFFRACTION100
3.3132-3.35660.36293190.31585539X-RAY DIFFRACTION100
3.3566-3.40240.41312820.32955533X-RAY DIFFRACTION100
3.4024-3.45080.42970.32135559X-RAY DIFFRACTION100
3.4508-3.5020.38222900.31065629X-RAY DIFFRACTION100
3.502-3.55640.36342820.30795518X-RAY DIFFRACTION100
3.5564-3.61440.38572990.31235528X-RAY DIFFRACTION100
3.6144-3.67630.37952770.31075560X-RAY DIFFRACTION100
3.6763-3.74280.36292890.31155574X-RAY DIFFRACTION100
3.7428-3.81430.39733000.30895579X-RAY DIFFRACTION100
3.8143-3.89160.36612930.30125571X-RAY DIFFRACTION100
3.8916-3.97550.35662860.29265589X-RAY DIFFRACTION100
3.9755-4.06730.36212980.29175535X-RAY DIFFRACTION100
4.0673-4.16810.3712840.2835603X-RAY DIFFRACTION100
4.1681-4.27970.32293080.29255556X-RAY DIFFRACTION100
4.2797-4.40430.32762840.27715541X-RAY DIFFRACTION100
4.4043-4.54490.36742870.28025597X-RAY DIFFRACTION100
4.5449-4.70530.35343040.28495558X-RAY DIFFRACTION100
4.7053-4.8910.33892930.27715583X-RAY DIFFRACTION100
4.891-5.11010.34922930.26235607X-RAY DIFFRACTION100
5.1101-5.37450.32582910.2665543X-RAY DIFFRACTION100
5.3745-5.70390.34872860.26395612X-RAY DIFFRACTION100
5.7039-6.13250.34842960.25355622X-RAY DIFFRACTION100
6.1325-6.72810.30963030.24065585X-RAY DIFFRACTION100
6.7281-7.65340.28052890.21775638X-RAY DIFFRACTION100
7.6534-9.46850.2222960.18965652X-RAY DIFFRACTION100
9.4685-19.97920.30092800.23865548X-RAY DIFFRACTION97

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