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- PDB-4zit: Crystal structure of AcrB in P21 space group -

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Basic information

Entry
Database: PDB / ID: 4zit
TitleCrystal structure of AcrB 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 / 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
NICKEL (II) ION / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.296 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)685,23115
Polymers681,9916
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)342,6458
Polymers340,9963
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)342,5867
Polymers340,9963
Non-polymers1,5914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.840, 156.856, 218.582
Angle α, β, γ (deg.)90.00, 92.70, 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 / Acriflavine ...AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B / Acriflavine resistance protein B


Mass: 113665.180 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: 3.81 Å3/Da / Density % sol: 67.74 %
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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.29→127.01 Å / Num. obs: 153515 / % possible obs: 100 % / Redundancy: 14.7 % / Net I/σ(I): 10.4
Reflection shellResolution: 3.29→3.47 Å / Redundancy: 14 % / Mean I/σ(I) obs: 2.1 / % 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: 3.296→19.945 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3386 7652 5.02 %
Rwork0.2682 --
obs0.2717 152521 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.296→19.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47560 0 213 0 47773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01448706
X-RAY DIFFRACTIONf_angle_d1.79666127
X-RAY DIFFRACTIONf_dihedral_angle_d16.6517619
X-RAY DIFFRACTIONf_chiral_restr0.0737795
X-RAY DIFFRACTIONf_plane_restr0.0088426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2962-3.33340.41681990.34373920X-RAY DIFFRACTION81
3.3334-3.37250.40032560.34394916X-RAY DIFFRACTION100
3.3725-3.41340.42392840.33344828X-RAY DIFFRACTION100
3.4134-3.45640.38792290.31784838X-RAY DIFFRACTION100
3.4564-3.50160.39852390.32364817X-RAY DIFFRACTION100
3.5016-3.54930.37772640.30364856X-RAY DIFFRACTION100
3.5493-3.59980.38042660.29594816X-RAY DIFFRACTION100
3.5998-3.65320.36862550.30344878X-RAY DIFFRACTION100
3.6532-3.70990.39732720.31514842X-RAY DIFFRACTION100
3.7099-3.77030.39382310.30644850X-RAY DIFFRACTION100
3.7703-3.83490.36752730.30384863X-RAY DIFFRACTION100
3.8349-3.90410.36072650.29764830X-RAY DIFFRACTION100
3.9041-3.97860.36962560.30144869X-RAY DIFFRACTION100
3.9786-4.05920.3622420.2974846X-RAY DIFFRACTION100
4.0592-4.14670.36332590.29914843X-RAY DIFFRACTION100
4.1467-4.24220.37362690.30864847X-RAY DIFFRACTION100
4.2422-4.34720.37382590.29254886X-RAY DIFFRACTION100
4.3472-4.46350.31242550.27424873X-RAY DIFFRACTION100
4.4635-4.59330.35692490.27474834X-RAY DIFFRACTION100
4.5933-4.73970.34742580.27354880X-RAY DIFFRACTION100
4.7397-4.90660.36792580.2744874X-RAY DIFFRACTION100
4.9066-5.09990.31232460.26354872X-RAY DIFFRACTION100
5.0999-5.32780.36112630.26744849X-RAY DIFFRACTION100
5.3278-5.60280.32832660.2584889X-RAY DIFFRACTION100
5.6028-5.94510.33862540.24454840X-RAY DIFFRACTION100
5.9451-6.39010.32782490.2284882X-RAY DIFFRACTION100
6.3901-7.00770.29582650.22694899X-RAY DIFFRACTION100
7.0077-7.96470.27532610.21174916X-RAY DIFFRACTION100
7.9647-9.83050.26582600.1994907X-RAY DIFFRACTION100
9.8305-19.94530.29712500.24514809X-RAY DIFFRACTION96

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