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- PDB-7mh6: Structure of EmrE-D3 mutant in complex with monobody L10 in low p... -

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Basic information

Entry
Database: PDB / ID: 7mh6
TitleStructure of EmrE-D3 mutant in complex with monobody L10 in low pH (protonated state)
Components
  • Monobody L10
  • Multidrug transporter EmrE
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / small multidrug resistance transporter / TRANSPORT PROTEIN-IMMUNE SYSTEM complex / EmrE / proton bound
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 speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsKermani, A.A. / Stockbridge, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1845012 United States
CitationJournal: Elife / Year: 2022
Title: Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates.
Authors: Kermani, A.A. / Burata, O.E. / Koff, B.B. / Koide, A. / Koide, S. / Stockbridge, R.B.
History
DepositionApr 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Monobody L10
B: Multidrug transporter EmrE
C: Monobody L10
A: Multidrug transporter EmrE


Theoretical massNumber of molelcules
Total (without water)43,4804
Polymers43,4804
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-42 kcal/mol
Surface area20330 Å2
Unit cell
Length a, b, c (Å)140.641, 49.850, 109.830
Angle α, β, γ (deg.)90.000, 93.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Monobody L10


Mass: 9832.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Multidrug transporter EmrE / Efflux-multidrug resistance protein EmrE / Ethidium resistance protein / Methyl viologen resistance protein C


Mass: 11907.279 Da / Num. of mol.: 2 / Mutation: E25N, W31I, V34M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: emrE, eb, mvrC, b0543, JW0531 / Production host: Escherichia coli (E. coli) / References: UniProt: P23895
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 4.37 Å3/Da / Density % sol: 71.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium chloride, 100 mM sodium cacodylate, pH 5.5, 34% PEG600

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.85→70.17 Å / Num. obs: 11183 / % possible obs: 87 % / Redundancy: 6.4 % / CC1/2: 0.994 / Net I/σ(I): 9.5
Reflection shellResolution: 2.85→3.16 Å / Redundancy: 7.1 % / Num. unique obs: 560 / CC1/2: 0.366 / % possible all: 62.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
STARANISOdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6WK8

6wk8


Resolution: 2.85→35.08 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 43.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.33 553 4.96 %
Rwork0.3087 10597 -
obs0.3096 11171 61.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.23 Å2 / Biso mean: 94.98 Å2 / Biso min: 43.33 Å2
Refinement stepCycle: final / Resolution: 2.85→35.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 0 1 2949
Biso mean---54.11 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.85-2.950.5191250.41394785.76
3.14-3.60.4328770.3877178842
3.6-4.530.34572250.332405095

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