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- PDB-2gif: Asymmetric structure of trimeric AcrB from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2gif
TitleAsymmetric structure of trimeric AcrB from Escherichia coli
ComponentsAcriflavine resistance protein B
KeywordsMEMBRANE PROTEIN/TRANSPORT PROTEIN / membrane protein / secondary transport / RND / antibiotic resistance / drug-efflux pump / alternating site mechanism / MEMBRANE PROTEIN-TRANSPORT PROTEIN COMPLEX
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
CITRATE ANION / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSeeger, M.A. / Schiefner, A. / Eicher, T. / Verrey, F. / Diederichs, K. / Pos, K.M.
CitationJournal: Science / Year: 2006
Title: Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism.
Authors: Seeger, M.A. / Schiefner, A. / Eicher, T. / Verrey, F. / Diederichs, K. / Pos, K.M.
History
DepositionMar 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acriflavine resistance protein B
B: Acriflavine resistance protein B
C: Acriflavine resistance protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,5875
Polymers344,2093
Non-polymers3782
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19620 Å2
ΔGint-84 kcal/mol
Surface area115550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.800, 134.100, 161.010
Angle α, β, γ (deg.)90.00, 98.21, 90.00
Int Tables number5
Space group name H-MC121
DetailsBiological assembly is a trimer as found in the asymmetric unit.

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Components

#1: Protein Acriflavine resistance protein B


Mass: 114736.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acrB, acrE / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P31224
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7

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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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 4.6
Details: 5% PEG 400, 16-22% PEG 300, 8-11% glycerol, 70mM sodium citrate, pH 4.6, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 29, 2005
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 103912 / Num. obs: 103134 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.4
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 1.6 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IWG

1iwg


Resolution: 2.9→29.51 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 46.735 / SU ML: 0.381 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.67 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26677 5177 5 %RANDOM
Rwork0.22551 ---
obs0.22761 98361 99.77 %-
all-98361 --
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: 73.945 Å2
Baniso -1Baniso -2Baniso -3
1-6.21 Å20 Å24.25 Å2
2---3.26 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23624 0 26 0 23650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02224101
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.96832729
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14853105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38624.535946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.854154053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.57515112
X-RAY DIFFRACTIONr_chiral_restr0.0690.23850
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0217886
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.212389
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.216953
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2732
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1941.515777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.35224852
X-RAY DIFFRACTIONr_scbond_it0.45739314
X-RAY DIFFRACTIONr_scangle_it0.7834.57877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 383 -
Rwork0.343 7154 -
obs--99.77 %
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)
12.16920.5919-1.8451.72160.08892.24010.0184-0.1703-0.03110.3742-0.0220.4540.0003-0.7110.0036-0.1054-0.08030.08240.4343-0.02720.0592-100.3867.0646-41.4258
25.0916-1.7297-3.49859.30671.55823.6404-0.2727-0.2757-0.32190.0481-0.0582-0.03070.1640.20810.3309-0.5730.0106-0.3031-0.47780.0665-0.6301-51.74944.2427-55.9539
32.0611.7647-1.05685.837-1.012.24670.00720.3481-0.2241-0.395-0.00920.5301-0.1173-0.53770.002-0.35710.033-0.152-0.32070.0093-0.4157-68.815914.2885-73.0812
41.41161.59420.34692.86260.44192.0734-0.14870.1921-0.0701-0.7604-0.0864-0.4873-0.16450.25190.2351-0.0399-0.01430.2623-0.48710.1362-0.2291-38.954325.1615-81.9689
513.63760.3374-3.85324.4903-0.00154.2951-0.1778-0.2-1.42980.0323-0.24330.18790.9311-0.8980.42120.0639-0.18920.0187-0.2023-0.1294-0.0517-74.121-5.5474-76.0597
65.72633.65280.05057.3556-0.17183.9806-0.1099-0.2375-0.820.1231-0.1340.48270.8213-0.59610.24390.1582-0.10850.2331-0.4680.0067-0.137-58.7533-18.8737-57.4653
71.6825-1.8118-0.33334.32450.41521.841-0.06110.0898-0.0582-0.45160.0117-0.71750.280.49860.0494-0.06010.08470.2894-0.44790.042-0.2219-36.67383.6525-80.4419
81.16490.3996-0.60471.2056-0.43871.9049-0.0607-0.0525-0.5154-0.0314-0.04590.42570.4879-0.64090.10660.2142-0.37330.18060.4104-0.00890.2787-102.8791-12.5945-39.1574
92.1434-0.2296-1.38531.60990.3381.18780.0958-0.39120.21530.2895-0.06170.2481-0.415-0.2709-0.03410.21060.2330.22190.1905-0.0962-0.0229-85.314838.8076-21.2781
104.941.2331-4.07911.7849-1.63036.30530.2355-0.42970.12110.3363-0.2631-0.2101-0.62790.20340.0276-0.25570.0492-0.0961-0.574-0.0059-0.434-53.879727.248-57.7248
115.48521.3399-4.39883.0837-1.44745.93540.0854-0.58490.05490.4462-0.0212-0.1378-0.59130.3576-0.06420.1843-0.0561-0.0789-0.1682-0.1239-0.0859-44.4143.7725-37.0384
121.1995-1.58591.13874.8493-1.58921.19820.0303-0.34790.11190.1651-0.3067-0.9203-0.43851.04980.2763-0.1959-0.1696-0.06330.07350.14190.1101-19.1829.0262-53.4877
136.8997-0.7872-5.10631.58330.37995.14120.11440.0720.5530.0069-0.02970.5831-0.7624-0.5422-0.08470.47170.02950.0682-0.2682-0.09030.169-55.252958.6469-49.0261
145.9952-2.3457-0.51315.37730.38322.70590.1467-0.21910.3681-0.17150.02990.6529-0.7248-0.7368-0.1766-0.02180.20410.0067-0.4570.117-0.1756-69.268642.6638-68.5203
151.5980.29160.14611.2206-1.38142.78350.0551-0.0830.1323-0.3591-0.1819-0.7428-0.06720.62280.1268-0.0775-0.16780.1475-0.40350.0358-0.0788-30.501337.8735-69.9169
162.26270.5033-0.84711.24080.03141.00170.1297-0.00430.56220.0583-0.0020.4716-0.4684-0.5726-0.12770.29920.43820.24050.34340.03480.3257-98.276647.3255-33.5011
1727.61111.253532.757516.97353.986939.23270.5338-0.1338-0.4593-0.6980.5133-0.93442.2032-0.9524-1.0470.4450.06370.50460.41290.28090.7133-125.47635.0083-29.6943
182.29390.568-0.99691.5571-0.42481.9128-0.1523-0.3708-0.20160.4668-0.0110.33710.1268-0.25030.16330.14170.04920.10850.25240.1353-0.2709-77.8867-1.1021-9.1237
1910.87842.3014-1.08342.3244-1.66772.2892-0.2896-0.17380.2757-0.0510.0582-0.446-0.34810.40510.2314-0.1576-0.0227-0.2664-0.27910.0024-0.3358-43.387619.1419-39.091
201.0656-1.1741-1.49664.41160.85184.0271-0.319-0.3621-0.39620.4389-0.0077-0.25910.78440.36150.3267-0.07890.1067-0.0981-0.14660.2895-0.1122-41.8976-8.8114-36.9241
211.25490.01310.65631.49530.58453.4132-0.09530.0439-0.4696-0.22280.1169-0.81870.30461.0196-0.0216-0.13250.17180.2324-0.21470.10220.0859-25.7672-3.1814-65.0639
225.55140.5336-1.1182.4289-0.77682.87670.0225-0.6881-0.04550.9897-0.0963-0.4696-0.0480.42370.07390.17020.2013-0.31220.31870.2375-0.0504-33.0466-3.4583-18.7362
232.9024-2.5853-1.54693.00262.28874.29440.0755-0.99040.15470.4164-0.3078-0.432-0.17070.69780.2323-0.0369-0.0762-0.48370.49010.0259-0.1875-35.011619.2787-16.8231
243.42850.38470.83682.70640.95871.6456-0.2257-0.21030.0641-0.19810.1727-1.0822-0.00861.04230.0529-0.31830.0733-0.00180.20910.16380.1839-16.02249.679-50.5677
252.46250.2144-1.7181.184-0.13082.91370.1128-0.7163-0.00850.6882-0.1240.2321-0.16680.05290.01120.37260.0340.03240.48680.0319-0.2906-71.07210.915.4936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 402 - 40
2X-RAY DIFFRACTION1AA325 - 502325 - 502
3X-RAY DIFFRACTION2AA41 - 13341 - 133
4X-RAY DIFFRACTION3AA134 - 180134 - 180
5X-RAY DIFFRACTION3AA272 - 324272 - 324
6X-RAY DIFFRACTION4AA181 - 271181 - 271
7X-RAY DIFFRACTION5AA570 - 672570 - 672
8X-RAY DIFFRACTION6AA673 - 723673 - 723
9X-RAY DIFFRACTION6AA812 - 859812 - 859
10X-RAY DIFFRACTION7AA724 - 811724 - 811
11X-RAY DIFFRACTION8AA503 - 569503 - 569
12X-RAY DIFFRACTION8AA860 - 1033860 - 1033
13X-RAY DIFFRACTION9BB2 - 402 - 40
14X-RAY DIFFRACTION9BB325 - 502325 - 502
15X-RAY DIFFRACTION10BB41 - 13341 - 133
16X-RAY DIFFRACTION11BB134 - 180134 - 180
17X-RAY DIFFRACTION11BB272 - 324272 - 324
18X-RAY DIFFRACTION12BB181 - 271181 - 271
19X-RAY DIFFRACTION13BB570 - 672570 - 672
20X-RAY DIFFRACTION14BB673 - 723673 - 723
21X-RAY DIFFRACTION14BB812 - 859812 - 859
22X-RAY DIFFRACTION15BB724 - 811724 - 811
23X-RAY DIFFRACTION16BB503 - 569503 - 569
24X-RAY DIFFRACTION16BB860 - 1033860 - 1033
25X-RAY DIFFRACTION17BB1034 - 10451034 - 1045
26X-RAY DIFFRACTION18CC2 - 402 - 40
27X-RAY DIFFRACTION18CC325 - 502325 - 502
28X-RAY DIFFRACTION19CC41 - 13341 - 133
29X-RAY DIFFRACTION20CC134 - 180134 - 180
30X-RAY DIFFRACTION20CC272 - 324272 - 324
31X-RAY DIFFRACTION21CC181 - 271181 - 271
32X-RAY DIFFRACTION22CC570 - 672570 - 672
33X-RAY DIFFRACTION23CC673 - 723673 - 723
34X-RAY DIFFRACTION23CC812 - 859812 - 859
35X-RAY DIFFRACTION24CC724 - 811724 - 811
36X-RAY DIFFRACTION25CC503 - 569503 - 569
37X-RAY DIFFRACTION25CC860 - 1033860 - 1033

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