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- PDB-4ziw: Crystal structure of AcrB deletion mutant in P21 space group -

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Basic information

Entry
Database: PDB / ID: 4ziw
TitleCrystal structure of AcrB deletion 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 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
NICKEL (II) ION / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.399 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)681,75315
Polymers678,5136
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)340,9068
Polymers339,2573
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)340,8477
Polymers339,2573
Non-polymers1,5914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.073, 157.781, 219.391
Angle α, β, γ (deg.)90.00, 93.14, 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: 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: 3.87 Å3/Da / Density % sol: 68.24 %
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: I02 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.399→109.55 Å / Num. obs: 142337 / % possible obs: 100 % / Redundancy: 17.4 % / Net I/σ(I): 14.3
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 17.1 % / Mean I/σ(I) obs: 2.4 / % 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: 3.399→19.998 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3493 7070 5 %
Rwork0.2749 --
obs0.2787 141395 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.399→19.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47319 0 213 0 47532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01548455
X-RAY DIFFRACTIONf_angle_d1.8965801
X-RAY DIFFRACTIONf_dihedral_angle_d16.79917538
X-RAY DIFFRACTIONf_chiral_restr0.0777773
X-RAY DIFFRACTIONf_plane_restr0.0098380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3987-3.43710.38362280.33654335X-RAY DIFFRACTION97
3.4371-3.47740.44032240.34324487X-RAY DIFFRACTION100
3.4774-3.51950.44382510.35044442X-RAY DIFFRACTION100
3.5195-3.56380.43182160.33174453X-RAY DIFFRACTION100
3.5638-3.61050.39262400.32064498X-RAY DIFFRACTION100
3.6105-3.65960.38232460.31024471X-RAY DIFFRACTION100
3.6596-3.71160.42982380.32414481X-RAY DIFFRACTION100
3.7116-3.76660.38012330.30424475X-RAY DIFFRACTION100
3.7666-3.82510.38232420.29944424X-RAY DIFFRACTION100
3.8251-3.88740.39152230.30454481X-RAY DIFFRACTION100
3.8874-3.95390.37242100.30214493X-RAY DIFFRACTION100
3.9539-4.02520.38932530.30224464X-RAY DIFFRACTION100
4.0252-4.1020.36562400.29544480X-RAY DIFFRACTION100
4.102-4.1850.38222300.30024449X-RAY DIFFRACTION100
4.185-4.27510.37912320.30124543X-RAY DIFFRACTION100
4.2751-4.37350.37322290.2934456X-RAY DIFFRACTION100
4.3735-4.48170.37372370.2914507X-RAY DIFFRACTION100
4.4817-4.60150.35822460.28434436X-RAY DIFFRACTION100
4.6015-4.73510.35822440.27444510X-RAY DIFFRACTION100
4.7351-4.88580.36982340.294462X-RAY DIFFRACTION100
4.8858-5.05770.38342260.28094488X-RAY DIFFRACTION100
5.0577-5.25670.3622540.28014489X-RAY DIFFRACTION100
5.2567-5.49120.3642340.2834493X-RAY DIFFRACTION100
5.4912-5.77410.37722440.27184487X-RAY DIFFRACTION100
5.7741-6.12610.36052290.27134515X-RAY DIFFRACTION100
6.1261-6.58340.38882340.26674499X-RAY DIFFRACTION100
6.5834-7.21750.33652450.2484514X-RAY DIFFRACTION100
7.2175-8.19830.28092340.21054523X-RAY DIFFRACTION100
8.1983-10.10230.23582480.19884534X-RAY DIFFRACTION100
10.1023-19.99810.29242260.25214436X-RAY DIFFRACTION96

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