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- PDB-3b61: EmrE multidrug transporter, apo crystal form -

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Basic information

Entry
Database: PDB / ID: 3b61
TitleEmrE multidrug transporter, apo crystal form
ComponentsMultidrug transporter emrE
KeywordsMEMBRANE PROTEIN / HELICAL MEMBRANE PROTEIN / MULTIDRUG RESISTANCE TRANSPORTER / SMR / Antiport / Inner membrane / Transmembrane
Function / homology
Function and homology information


EmrE multidrug transporter complex / amino-acid betaine transmembrane transporter activity / glycine betaine transport / choline transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / antiporter activity / response to osmotic stress / xenobiotic transport / transmembrane transporter activity ...EmrE multidrug transporter complex / amino-acid betaine transmembrane transporter activity / glycine betaine transport / choline transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / antiporter activity / response to osmotic stress / xenobiotic transport / transmembrane transporter activity / xenobiotic transmembrane transporter activity / xenobiotic metabolic process / transmembrane transport / cellular response to xenobiotic stimulus / response to xenobiotic stimulus / DNA damage response / identical protein binding / membrane / plasma membrane
Similarity search - Function
Small drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein
Similarity search - Domain/homology
Multidrug transporter EmrE
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4.5 Å
AuthorsChang, G. / Chen, Y.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: X-ray structure of EmrE supports dual topology model.
Authors: Chen, Y.J. / Pornillos, O. / Lieu, S. / Ma, C. / Chen, A.P. / Chang, G.
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: Multidrug transporter emrE
B: Multidrug transporter emrE
C: Multidrug transporter emrE
D: Multidrug transporter emrE
E: Multidrug transporter emrE
F: Multidrug transporter emrE
G: Multidrug transporter emrE
H: Multidrug transporter emrE


Theoretical massNumber of molelcules
Total (without water)95,7068
Polymers95,7068
Non-polymers00
Water00
1
A: Multidrug transporter emrE
B: Multidrug transporter emrE


Theoretical massNumber of molelcules
Total (without water)23,9272
Polymers23,9272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Multidrug transporter emrE
D: Multidrug transporter emrE


Theoretical massNumber of molelcules
Total (without water)23,9272
Polymers23,9272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Multidrug transporter emrE
F: Multidrug transporter emrE


Theoretical massNumber of molelcules
Total (without water)23,9272
Polymers23,9272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Multidrug transporter emrE
H: Multidrug transporter emrE


Theoretical massNumber of molelcules
Total (without water)23,9272
Polymers23,9272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.000, 239.200, 284.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein
Multidrug transporter emrE / Efflux-multidrug resistance protein emrE / Methyl viologen resistance protein C / Ethidium resistance protein / Coordinate model: Cα atoms only


Mass: 11963.278 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: emrE, eb, mvrC / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23895

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20 mM NaCl, 20 mM sodium acetate, 200-600 mM ammonium sulfate, 15-30% (w/v) PEG-200, and 0.3-0.6% (w/v) NG, pH 4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.0057, 1.0089, 1.0067
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00571
21.00891
31.00671
ReflectionResolution: 3→50 Å / Num. obs: 13836 / % possible obs: 75.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.096 / Net I/σ(I): 12.2
Reflection shellResolution: 4.5→4.66 Å / Num. unique all: 1584 / % possible all: 38.2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 4.5→19.99 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: The structure contains CA atoms only.
RfactorNum. reflection% reflectionSelection details
Rfree0.362 1369 -RANDOM
Rwork0.318 ---
obs-13836 75.8 %-
Displacement parametersBiso mean: 262.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.06 Å20 Å20 Å2
2---16.89 Å20 Å2
3---10.83 Å2
Refinement stepCycle: LAST / Resolution: 4.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms856 0 0 0 856
LS refinement shellResolution: 4.5→4.78 Å / Rfactor Rfree error: 0.05
RfactorNum. reflection% reflection
Rfree0.548 120 -
Rwork0.492 --
obs-1032 38.2 %

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