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- PDB-3b5d: EmrE multidrug transporter in complex with TPP, C2 crystal form -

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Basic information

Entry
Database: PDB / ID: 3b5d
TitleEmrE multidrug transporter in complex with TPP, C2 crystal form
ComponentsMultidrug transporter emrE
KeywordsMEMBRANE PROTEIN / HELICAL MEMBRANE PROTEIN / MULTIDRUG RESISTANCE TRANSPORTER / SMR / Antiport / Inner membrane / Transmembrane / Joint Center for Innovative Membrane Protein Technologies
Function / homology
Function and homology information


EmrE multidrug transporter complex / choline transmembrane transporter activity / glycine betaine transport / amino-acid betaine transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / antiporter activity / response to osmotic stress / xenobiotic transmembrane transporter activity ...EmrE multidrug transporter complex / choline transmembrane transporter activity / glycine betaine transport / amino-acid betaine transmembrane transporter activity / choline transport / xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transport / antiporter activity / response to osmotic stress / xenobiotic transmembrane transporter activity / 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
TETRAPHENYLPHOSPHONIUM / Multidrug transporter EmrE
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.8 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 25, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Multidrug transporter emrE
B: Multidrug transporter emrE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2663
Polymers23,9272
Non-polymers3391
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.1, 43.7, 76.4
Angle α, β, γ (deg.)90, 108.1, 90
Int Tables number5
Space group name H-MC121

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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.: 2
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: pIVEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23895
#2: Chemical ChemComp-P4P / TETRAPHENYLPHOSPHONIUM


Mass: 339.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20P

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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: 3.82 Å3/Da / Density % sol: 67.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 100-200 mM calcium chloride, 100 mM Tris, 11-14% (w/v) PEG 2,000 MME , and 0.3-0.6% (w/v) NG, pH 6.8, 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: 0.9790, 0.9793, 0.9184
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2006 / Details: Mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.91841
ReflectionResolution: 3→50 Å / Num. all: 3077 / Num. obs: 3077 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 44.4 Å2 / Rsym value: 0.067 / Net I/σ(I): 22.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 0.7 / Num. unique all: 286 / Rsym value: 0.32 / % possible all: 34.3

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 3.8→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.364 335 -RANDOM
Rwork0.325 ---
all-3680 --
obs-3077 83.6 %-
Displacement parametersBiso mean: 201 Å2
Baniso -1Baniso -2Baniso -3
1-23.57 Å20 Å250.87 Å2
2--64.33 Å20 Å2
3----87.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.92 Å-
Luzzati d res low-20 Å
Luzzati sigma a1.02 Å-
Refinement stepCycle: LAST / Resolution: 3.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms199 0 25 0 224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_deg1.35
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.077
RfactorNum. reflection% reflection
Rfree0.512 44 -
Rwork0.468 --
obs-286 55.7 %

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