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- PDB-6nzi: Low resolution crystal structure of the bacterial multidrug efflu... -

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Basic information

Entry
Database: PDB / ID: 6nzi
TitleLow resolution crystal structure of the bacterial multidrug efflux transporter AcrB in the presence of cadmium
ComponentsEfflux pump membrane transporter
KeywordsMEMBRANE PROTEIN / efflux pump / cadmium
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / : / Efflux pump membrane transporter
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.44 Å
AuthorsSmith, A.T. / Rosenzweig, A.C.
CitationJournal: To Be Published
Title: Low resolution crystal structure of the bacterial multidrug efflux transporter AcrB in the presence of cadmium
Authors: Smith, A.T. / Rosenzweig, A.C.
History
DepositionFeb 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8903
Polymers113,6651
Non-polymers2252
Water00
1
A: Efflux pump membrane transporter
hetero molecules

A: Efflux pump membrane transporter
hetero molecules

A: Efflux pump membrane transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,6709
Polymers340,9963
Non-polymers6746
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area20850 Å2
ΔGint-117 kcal/mol
Surface area116540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.280, 144.280, 519.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Efflux pump membrane transporter


Mass: 113665.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acrB / Production host: Escherichia coli (E. coli) / References: UniProt: E2QH56
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd

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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: 4.58 Å3/Da / Density % sol: 73.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Tris, pH=7.5, 250 mM choline chloride, 10% PEG 2K MME, 5 mM CdSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 4.44→19.797 Å / Num. obs: 13142 / % possible obs: 98.45 % / Redundancy: 8.9 % / CC1/2: 0.998 / Net I/σ(I): 11
Reflection shellResolution: 4.44→4.597 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1297 / CC1/2: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
MrBUMPphasing
RefinementResolution: 4.44→19.797 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.29
RfactorNum. reflection% reflection
Rfree0.3199 674 5.13 %
Rwork0.2599 --
obs0.2629 13133 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 469.91 Å2 / Biso mean: 190.0348 Å2 / Biso min: 68.79 Å2
Refinement stepCycle: final / Resolution: 4.44→19.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7715 0 1 0 7716
Biso mean--311.95 --
Num. residues----1012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.4401-4.77840.35161460.283924422588100
4.7784-5.25120.33681240.277924652589100
5.2512-5.99250.34711390.30524752614100
5.9925-7.48150.39671290.292424972626100
7.4815-19.79760.26041360.2212580271699
Refinement TLS params.Method: refined / Origin x: 46.6171 Å / Origin y: 42.7571 Å / Origin z: 56.7389 Å
111213212223313233
T0.5393 Å20.1292 Å2-0.1159 Å2-0.9693 Å20.1477 Å2--0.8436 Å2
L0.0572 °20.1281 °2-0.4175 °2-0.4667 °2-0.2743 °2--1.7795 °2
S0.0176 Å °0.0468 Å °0.1689 Å °0.0288 Å °-0.0265 Å °0.1776 Å °0.1091 Å °-0.1576 Å °0.0367 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 1033
2X-RAY DIFFRACTION1allB1 - 2

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