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- PDB-6vrz: protein A -

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Basic information

Entry
Database: PDB / ID: 6vrz
Titleprotein A
ComponentsMultidrug transporter MdfA
KeywordsTRANSPORT PROTEIN/ANTIBIOTIC / membrane protein / TRANSPORT PROTEIN-ANTIBIOTIC 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 / response to antibiotic / plasma membrane
Similarity search - Function
Sugar transporter, conserved site / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
CHLORAMPHENICOL / PRASEODYMIUM ION / Multidrug transporter MdfA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLu, M. / Lu, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094195 United States
CitationJournal: Sci Rep / Year: 2020
Title: Structure and mechanism of a redesigned multidrug transporter from the Major Facilitator Superfamily.
Authors: Wu, H.H. / Symersky, J. / Lu, M.
History
DepositionFeb 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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 MdfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5284
Polymers41,9231
Non-polymers6053
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.048, 65.215, 111.462
Angle α, β, γ (deg.)90.000, 111.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Multidrug transporter MdfA / Chloramphenicol resistance pump Cmr


Mass: 41923.020 Da / Num. of mol.: 1 / Mutation: E26T/D34M/A150E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mdfA, cmlA, cmr, b0842, JW0826 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEY8
#2: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
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: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG, salts, magnesium, etc

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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: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 39352 / % possible obs: 95 % / Redundancy: 7 % / CC1/2: 1 / Rsym value: 0.09 / Net I/σ(I): 31
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 300 / CC1/2: 0.36 / Rsym value: 0.67 / % possible all: 77

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Processing

Software
NameVersionClassification
REFMAC2.1refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→15 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.233 --
Rwork0.22 --
obs0.226 39352 90 %
Displacement parametersBiso max: 166.35 Å2 / Biso mean: 52.9607 Å2 / Biso min: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 22 111 3070

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