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- PDB-6oop: protein B -

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Basic information

Entry
Database: PDB / ID: 6oop
Titleprotein B
ComponentsMultidrug transporter MdfA
KeywordsTRANSPORT PROTEIN / Complex / Transport
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 / transmembrane transporter activity / response to antibiotic / plasma membrane
Similarity search - Function
Sugar transport proteins signature 1. / 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
1,1'-dimethyl-4,4'-bipyridin-1-ium / PRASEODYMIUM ION / Multidrug transporter MdfA / Multidrug transporter MdfA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug transporter MdfA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9614
Polymers42,4931
Non-polymers4683
Water99155
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)85,9218
Polymers84,9852
Non-polymers9366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2250 Å2
ΔGint-49 kcal/mol
Surface area30740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.068, 63.149, 102.074
Angle α, β, γ (deg.)90.00, 100.87, 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
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-KHJ / 1,1'-dimethyl-4,4'-bipyridin-1-ium


Mass: 186.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PR / PRASEODYMIUM ION / Praseodymium


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.54 Å3/Da / Density % sol: 65.26 %
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: 2.8→15 Å / Num. obs: 12656 / % possible obs: 91 % / Redundancy: 5 % / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.9 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: 2.8→15 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs12656 90 %
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 0 16 55 3007

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