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- PDB-4u96: Coupling of remote alternating-access transport mechanisms for pr... -

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Basic information

Entry
Database: PDB / ID: 4u96
TitleCoupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB
Components
  • DARPin
  • Multidrug efflux pump subunit AcrB
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / DARPin / multidrug efflux 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 / membrane / identical protein binding / 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 / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPos, K.M.
CitationJournal: elife / Year: 2014
Title: Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB
Authors: Eicher, T. / Seeger, M.A. / Anselmi, C. / Zhou, W. / Brandstaetter, L. / Verrey, F. / Diederichs, K. / Faraldo-Gomez, J.D. / Pos, K.M.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: DARPin
E: DARPin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,16012
Polymers380,5865
Non-polymers3,5747
Water42,6602368
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28650 Å2
ΔGint-95 kcal/mol
Surface area124300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.790, 160.770, 246.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Multidrug efflux pump subunit AcrB / AcrAB-TolC multidrug efflux pump subunit AcrB / Acridine resistance protein B


Mass: 114650.180 Da / Num. of mol.: 3 / Mutation: R971A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P31224
#2: Protein DARPin /


Mass: 18317.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2368 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M ADA, pH 6.5, 0.2 M (NH4)2SO4, 9% PEG4000, 7.3% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.2→48.9 Å / Num. obs: 290078 / % possible obs: 99.35 % / Redundancy: 8.5 % / Net I/σ(I): 7.74
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 7.2 % / Rmerge(I) obs: 2.726 / Mean I/σ(I) obs: 0.8 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.5.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dx5

4dx5


Resolution: 2.2→48.901 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 14506 5 %
Rwork0.1958 --
obs0.1983 290058 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25951 0 237 2368 28556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826688
X-RAY DIFFRACTIONf_angle_d1.1736240
X-RAY DIFFRACTIONf_dihedral_angle_d15.7419720
X-RAY DIFFRACTIONf_chiral_restr0.0454293
X-RAY DIFFRACTIONf_plane_restr0.0054613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.39484290.35628133X-RAY DIFFRACTION89
2.225-2.25120.37174660.33638860X-RAY DIFFRACTION97
2.2512-2.27860.34934810.30689124X-RAY DIFFRACTION99
2.2786-2.30750.35694800.30869136X-RAY DIFFRACTION100
2.3075-2.33780.34464800.29729105X-RAY DIFFRACTION100
2.3378-2.36990.33274810.29569168X-RAY DIFFRACTION100
2.3699-2.40370.33944820.2749131X-RAY DIFFRACTION100
2.4037-2.43960.31444810.26889152X-RAY DIFFRACTION100
2.4396-2.47770.31854810.2659130X-RAY DIFFRACTION100
2.4777-2.51830.32024840.24919205X-RAY DIFFRACTION100
2.5183-2.56180.29694830.23679155X-RAY DIFFRACTION100
2.5618-2.60830.29164820.23639169X-RAY DIFFRACTION100
2.6083-2.65850.28954810.23089151X-RAY DIFFRACTION100
2.6585-2.71280.27844850.22139205X-RAY DIFFRACTION100
2.7128-2.77170.28674830.2149177X-RAY DIFFRACTION100
2.7717-2.83620.27754840.21539190X-RAY DIFFRACTION100
2.8362-2.90710.25844830.20139194X-RAY DIFFRACTION100
2.9071-2.98570.25394860.19079224X-RAY DIFFRACTION100
2.9857-3.07360.25594840.18759185X-RAY DIFFRACTION100
3.0736-3.17280.23814870.17959254X-RAY DIFFRACTION100
3.1728-3.28610.23024880.17199251X-RAY DIFFRACTION100
3.2861-3.41770.22174860.16769251X-RAY DIFFRACTION100
3.4177-3.57320.21534860.1599245X-RAY DIFFRACTION100
3.5732-3.76150.18564880.1519251X-RAY DIFFRACTION100
3.7615-3.99710.19364880.1499281X-RAY DIFFRACTION100
3.9971-4.30550.1964910.15219334X-RAY DIFFRACTION100
4.3055-4.73850.1944920.1479337X-RAY DIFFRACTION100
4.7385-5.42340.19064930.14929383X-RAY DIFFRACTION100
5.4234-6.82990.24174980.17549458X-RAY DIFFRACTION100
6.8299-48.91280.21255130.18819713X-RAY DIFFRACTION100
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)
10.5340.1151-0.21630.3275-0.06280.69290.1384-0.00660.28460.0273-0.00410.0808-0.3489-0.0458-0.04310.30650.01110.08070.1886-0.03130.305229.8178-15.2256-16.9832
20.3225-0.05660.07260.2723-0.2030.41470.03570.18540.0171-0.1098-0.03070.03650.0714-0.0791-0.00980.21430.0072-0.02940.292-0.03330.25728.9518-42.9613-52.0915
30.45540.1317-0.11350.1831-0.11790.55490.04120.03260.0237-0.0072-0.0143-0.0003-0.06820.0711-0.01420.1522-0.0010.00470.15320.00220.188867.5852-27.4957-34.2897
41.19230.03780.6810.9356-0.05461.7179-0.04550.0314-0.00160.00270.0170.1974-0.0342-0.25010.04260.2789-0.1488-0.00910.3575-0.0770.40710.8086-74.8853-23.4653
50.8592-0.3481-0.09521.68020.24151.15870.0052-0.44290.19860.40280.0369-0.3278-0.23370.069-0.04090.4385-0.1414-0.03840.7451-0.10980.262146.7657-38.474828.0186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E

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