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- PDB-6ooq: protein C -

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Basic information

Entry
Database: PDB / ID: 6ooq
Titleprotein C
ComponentsMultidrug transporter MdfA
KeywordsTRANSPORT PROTEIN / Complex
Function / homology
Function and homology information


potassium:proton antiporter activity / sodium:proton antiporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / regulation of cellular pH / xenobiotic transmembrane transporter activity / transmembrane transporter activity / response to antibiotic / integral component of plasma membrane / integral component of membrane / plasma membrane
Similarity search - Function
Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily (MFS) profile. / Major facilitator superfamily domain / MFS transporter superfamily
Similarity search - Domain/homology
Multidrug efflux MFS transporter MdfA / Multidrug transporter MdfA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsLu, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094195 United States
CitationJournal: Commun Biol / Year: 2019
Title: Structure of an engineered multidrug transporter MdfA reveals the molecular basis for substrate recognition.
Authors: Wu, H.H. / Symersky, J. / Lu, M.
History
DepositionApr 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug transporter MdfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8852
Polymers42,4931
Non-polymers3931
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Multidrug transporter MdfA
hetero molecules

A: Multidrug transporter MdfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7704
Polymers84,9852
Non-polymers7852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2760 Å2
ΔGint-14 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.477, 71.369, 113.142
Angle α, β, γ (deg.)90.00, 109.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Multidrug transporter MdfA


Mass: 42492.570 Da / Num. of mol.: 1 / Fragment: residues 9-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: A9R57_05385, BJJ90_17655 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E5MBX7, UniProt: P0AEY8*PLUS
#2: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID / Deoxycholic acid


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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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: 4.18 Å3/Da / Density % sol: 70.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 10817 / % possible obs: 98 % / Redundancy: 15 % / Net I/σ(I): 40
Reflection shellResolution: 3→3.1 Å / Num. unique obs: 300

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3→15 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs10817 98 %
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 28 0 2951

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