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- PDB-6gv1: Crystal structure of E.coli Multidrug/H+ antiporter MdfA in outwa... -

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Basic information

Entry
Database: PDB / ID: 6gv1
TitleCrystal structure of E.coli Multidrug/H+ antiporter MdfA in outward open conformation with bound Fab fragment
Components
  • Fab fragment YN1074 heavy chain
  • Fab fragment YN1074 light chain
  • Major Facilitator Superfamily multidrug/H+ antiporter MdfA from E.coli
KeywordsTRANSPORT PROTEIN / Major Facilitator Superfamily / multidrug resistance / proton transport / MFS transporter / drug proton antiporter
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Multidrug transporter MdfA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsNagarathinam, K. / Parthier, C. / Stubbs, M.T. / Tanabe, M.
Funding support Germany, Japan, 2items
OrganizationGrant numberCountry
Other governmentBMBF 03Z2HN21 Germany
Japan Agency for Medical Research and Development (AMED)JP18am0101071j0001 Japan
Citation
Journal: Nat Commun / Year: 2018
Title: Outward open conformation of a Major Facilitator Superfamily multidrug/H+antiporter provides insights into switching mechanism.
Authors: Nagarathinam, K. / Nakada-Nakura, Y. / Parthier, C. / Terada, T. / Juge, N. / Jaenecke, F. / Liu, K. / Hotta, Y. / Miyaji, T. / Omote, H. / Iwata, S. / Nomura, N. / Stubbs, M.T. / Tanabe, M.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: The multidrug-resistance transporter MdfA from Escherichia coli: crystallization and X-ray diffraction analysis.
Authors: Nagarathinam, K. / Jaenecke, F. / Nakada-Nakura, Y. / Hotta, Y. / Liu, K. / Iwata, S. / Stubbs, M.T. / Nomura, N. / Tanabe, M.
History
DepositionJun 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major Facilitator Superfamily multidrug/H+ antiporter MdfA from E.coli
H: Fab fragment YN1074 heavy chain
L: Fab fragment YN1074 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0634
Polymers92,9673
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-32 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.258, 73.258, 927.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Major Facilitator Superfamily multidrug/H+ antiporter MdfA from E.coli


Mass: 44349.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Plasmid: pWaldo-GFPe / Production host: Escherichia coli (E. coli) / Variant (production host): C43 (DE3) / References: UniProt: P0AEY8
#2: Antibody Fab fragment YN1074 heavy chain


Mass: 24984.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Fab fragment YN1074 light chain


Mass: 23632.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.87 Å3/Da / Density % sol: 68.18 % / Description: hexagonal
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.4
Details: 100 mM ADA pH 6.5 100 mM NaCl 100 mM Li2SO4 32-36% PEG 300 8.8 MAG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→49.048 Å / Num. obs: 22224 / % possible obs: 99.9 % / Redundancy: 17.3 % / Biso Wilson estimate: 109.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.254 / Rrim(I) all: 0.262 / Χ2: 0.988 / Net I/σ(I): 11.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.4-3.6116.0391.6691.5934230.5831.72499.9
3.61-3.8517.5981.0552.8532900.7911.087100
3.85-4.1616.6470.6874.6929960.9240.70999.8
4.16-4.5518.9330.3828.6128720.980.393100
4.55-5.0918.4640.25811.6225760.9940.266100
5.09-5.8617.8610.24111.8123250.9940.248100
5.86-7.1517.4140.1716.5120360.9960.17599.9
7.15-10.0116.7830.07334.9616300.9990.076100
10.01-49.04814.4220.03651.59107610.03898.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZP0, 1IBG

4zp0

1ibg


Resolution: 3.4→49.048 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.9
RfactorNum. reflection% reflection
Rfree0.2831 1112 5.01 %
Rwork0.2575 --
obs0.2588 22216 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 278.35 Å2 / Biso mean: 113.3094 Å2 / Biso min: 68.89 Å2
Refinement stepCycle: final / Resolution: 3.4→49.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6134 0 5 0 6139
Biso mean--136.84 --
Num. residues----806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036283
X-RAY DIFFRACTIONf_angle_d0.5968551
X-RAY DIFFRACTIONf_chiral_restr0.04994
X-RAY DIFFRACTIONf_plane_restr0.0041059
X-RAY DIFFRACTIONf_dihedral_angle_d11.1233698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.4005-3.55520.37581360.356625092645
3.5552-3.74260.36971320.312725682700
3.7426-3.9770.32211350.297525382673
3.977-4.28390.27311370.269225822719
4.2839-4.71460.26331330.232325942727
4.7146-5.39610.25271420.234726352777
5.3961-6.79570.30821400.249727012841
6.7957-49.05270.25831570.240229773134
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7532-0.127-0.22921.9133-0.10470.03810.06940.341-0.0635-0.1958-0.01180.0719-0.05620.0899-0.00541.30990.0238-0.0450.94330.01770.52695.825988.0966-0.1866
20.78781.01510.40373.35011.05692.3033-0.1868-0.3714-0.01311.2001-0.1311-0.22450.1939-0.0242-0.21251.5147-0.0275-0.12561.05390.02910.59888.521168.799316.2221
32.6617-0.9870.17143.4591-0.03920.68720.23220.21990.2008-0.3482-0.03810.02580.1312-0.1958-0.0261.2265-0.03550.01730.89960.05440.5604-15.538376.9829-0.2051
44.5882-1.30010.04892.80190.16172.964-0.055-0.80660.46960.13090.16370.1695-0.2122-0.1205-0.08921.60880.0436-0.10531.4412-0.06850.6942.257384.064238.5783
50.09740.11670.56630.14120.68243.31750.0251-0.81170.09630.81010.04230.1653-0.2595-0.1674-0.27512.327-0.22580.02332.44060.16150.7314-0.099985.82860.2634
60.7424-0.9863-0.52493.4151.57560.8440.3927-0.10640.3321-0.4552-0.0081-0.3179-0.4528-0.2354-0.23292.30540.1669-0.09052.57670.0810.938915.136279.844473.9501
73.4181-1.4734-1.65742.99081.33741.1210.0374-0.8898-0.5365-0.03470.10180.46610.56640.174-0.04551.61430.1151-0.08111.43030.14980.938117.943868.685236.9226
80.3604-0.430.45360.5103-0.5380.56940.2354-0.497-0.34580.5447-0.1939-0.1631-0.05150.2448-0.23381.98730.162-0.27111.93070.34550.673226.113163.892756.5492
91.8582-1.6145-0.07943.9133-0.21670.0307-0.34060.02870.21440.42950.01570.07040.28980.10440.09442.1057-0.2236-0.09582.59020.17390.921411.848163.758972.9327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 191 )A14 - 191
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 218 )A192 - 218
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 400 )A219 - 400
4X-RAY DIFFRACTION4chain 'H' and (resid 4 through 110 )H4 - 110
5X-RAY DIFFRACTION5chain 'H' and (resid 111 through 123 )H111 - 123
6X-RAY DIFFRACTION6chain 'H' and (resid 124 through 216 )H124 - 216
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 102 )L1 - 102
8X-RAY DIFFRACTION8chain 'L' and (resid 103 through 113 )L103 - 113
9X-RAY DIFFRACTION9chain 'L' and (resid 114 through 211 )L114 - 211

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