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- PDB-2w1b: The structure of the efflux pump AcrB in complex with bile acid -

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Basic information

Entry
Database: PDB / ID: 2w1b
TitleThe structure of the efflux pump AcrB in complex with bile acid
ComponentsACRIFLAVIN RESISTANCE PROTEIN B
KeywordsMEMBRANE PROTEIN / MULTIDRUG EFFLUX / MEMBRANE / TRANSPORT / TRANSPORTER
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
Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å
AuthorsDrew, D. / Klepsch, M.M. / Newstead, S. / Flaig, R. / De Gier, J.W. / Iwata, S. / Beis, K.
Citation
Journal: Mol.Membr.Biol. / Year: 2008
Title: The Structure of the Efflux Pump Acrb in Complex with Bile Acid.
Authors: Drew, D. / Klepsch, M.M. / Newstead, S. / Flaig, R. / De Gier, J.W. / Iwata, S. / Beis, K.
#1: Journal: Nature / Year: 2002
Title: Crystal Structure of Bacterial Multidrug Efflux Transporter Acrb.
Authors: Murakami, S. / Nakashima, R. / Yamashita, E. / Yamaguchi, A.
History
DepositionOct 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACRIFLAVIN RESISTANCE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0582
Polymers113,6651
Non-polymers3931
Water00
1
A: ACRIFLAVIN RESISTANCE PROTEIN B
hetero molecules

A: ACRIFLAVIN RESISTANCE PROTEIN B
hetero molecules

A: ACRIFLAVIN RESISTANCE PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,1736
Polymers340,9963
Non-polymers1,1783
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area23910 Å2
ΔGint-163.7 kcal/mol
Surface area141750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.490, 145.490, 515.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ACRIFLAVIN RESISTANCE PROTEIN B / ACRE


Mass: 113665.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BILE ACID, DEOXYCHOLATE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P31224
#2: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.64 Å3/Da / Density % sol: 73.53 % / Description: NONE
Crystal growpH: 7.5
Details: 10% PEG 4000, 0.1 M HEPES PH 7.5, 0.1 M AMMONIUM SULPHATE AND 22% V/V GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9697
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 10, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9697 Å / Relative weight: 1
ReflectionResolution: 3.85→57.45 Å / Num. obs: 19539 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 2.5
Reflection shellResolution: 3.85→4.02 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.3 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IWG

1iwg


Resolution: 3.85→40 Å / Cor.coef. Fo:Fc: 0.831 / Cor.coef. Fo:Fc free: 0.748 / SU B: 133.883 / SU ML: 0.832 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.904 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.34919 980 5 %RANDOM
Rwork0.27779 ---
obs0.28141 18545 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 75.719 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20.74 Å20 Å2
2--1.49 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 3.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7841 0 28 0 7869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228022
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.97210901
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56651031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.24724.537313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.645151344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7091537
X-RAY DIFFRACTIONr_chiral_restr0.090.21288
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025931
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.24209
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25462
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2319
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.2158
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3461.55262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.62828248
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.50733134
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8554.52653
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.85→3.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 60
Rwork0.307 1353
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1772-1.2315-2.0342.7506-0.79413.7411-0.3691-0.1554-0.3332-0.08830.25060.34470.7329-0.17050.11850.0031-0.2145-0.0153-0.2827-0.1023-0.0691-60.1536-16.6617-22.4287
20.92570.2857-0.00481.38450.31670.81250.0355-0.13360.30040.30080.00660.1587-0.16270.042-0.0421-0.027-0.02680.0734-0.11610.0337-0.3295-60.1379-21.9963-78.9584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 32
2X-RAY DIFFRACTION1A338 - 564
3X-RAY DIFFRACTION1A869 - 1033
4X-RAY DIFFRACTION2A33 - 336
5X-RAY DIFFRACTION2A565 - 866

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