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- PDB-7svx: Structure of EmrE-D3 mutant in complex with monobody L10 and harmane -

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Basic information

Entry
Database: PDB / ID: 7svx
TitleStructure of EmrE-D3 mutant in complex with monobody L10 and harmane
Components
  • L10 monobody
  • Multidrug transporter EmrE
KeywordsTRANSPORT PROTEIN / Small Multidrug Resistance transporters / drug efflux pump / EmrE / Membrane protein
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 / response to osmotic stress / antiporter activity / 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 / response to osmotic stress / antiporter activity / 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
1-methyl-9H-pyrido[3,4-b]indole / Multidrug transporter EmrE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 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
DepositionNov 19, 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
A: Multidrug transporter EmrE
C: L10 monobody
B: Multidrug transporter EmrE
D: L10 monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8615
Polymers43,6784
Non-polymers1821
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-39 kcal/mol
Surface area21230 Å2
Unit cell
Length a, b, c (Å)145.703, 51.837, 114.959
Angle α, β, γ (deg.)90.000, 92.680, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: 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
#2: Antibody L10 monobody


Mass: 9931.934 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)
#3: Chemical ChemComp-CN9 / 1-methyl-9H-pyrido[3,4-b]indole / harmane


Mass: 182.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.96 Å3/Da / Density % sol: 75.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.1 M ammonium sulfate, 0.1 M HEPES, pH 7.1, 33.8% 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: 0.9183 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 3.9→114.83 Å / Num. obs: 3378 / % possible obs: 82.1 % / Redundancy: 6.6 % / CC1/2: 0.991 / Net I/σ(I): 8.2
Reflection shellResolution: 3.921→4.65 Å / Redundancy: 6.7 % / Num. unique obs: 338 / CC1/2: 0.921 / % possible all: 69.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
STARANISOdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6WK8

6wk8


Resolution: 3.9→60.21 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 44.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3436 135 4.03 %
Rwork0.3416 3212 -
obs0.3407 3347 41.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.89 Å2 / Biso mean: 62.0083 Å2 / Biso min: 10.9 Å2
Refinement stepCycle: final / Resolution: 3.9→60.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 14 0 2935
Biso mean--30 --
Num. residues----382
LS refinement shellResolution: 3.9→4.041 Å / Num. reflection Rfree: 135 / Num. reflection Rwork: 24 / Rfactor Rfree error: 0

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