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- PDB-4zow: Crystal structure of E. coli multidrug transporter MdfA in comple... -

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Basic information

Entry
Database: PDB / ID: 4zow
TitleCrystal structure of E. coli multidrug transporter MdfA in complex with chloramphenicol
ComponentsMultidrug transporter MdfA
KeywordsTRANSPORT PROTEIN / MFS family / Multi-drug antiporter / MDFA / Cm
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 / Multidrug transporter MdfA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsZhang, X.C. / Heng, J. / Zhao, Y. / Wang, X.
CitationJournal: Cell Res. / Year: 2015
Title: Substrate-bound structure of the E. coli multidrug resistance transporter MdfA
Authors: Heng, J. / Zhao, Y. / Liu, M. / Liu, Y. / Fan, J. / Wang, X. / Zhao, Y. / Zhang, X.C.
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Data collection
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 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)42,7142
Polymers42,3911
Non-polymers3231
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-11 kcal/mol
Surface area16440 Å2
Unit cell
Length a, b, c (Å)93.852, 63.449, 99.726
Angle α, β, γ (deg.)90.000, 106.090, 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: 42390.543 Da / Num. of mol.: 1 / Fragment: UNP residues 10-400 / Mutation: Q122R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: mdfA, cmlA, cmr, b0842, JW0826
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0AEY8
#2: Chemical ChemComp-CLM / CHLORAMPHENICOL / Chloramphenicol


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: sodium acetate, PEG 400, magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 11.7 % / Number: 135599 / Rmerge(I) obs: 0.142 / Χ2: 1.03 / D res high: 3 Å / D res low: 50 Å / Num. obs: 11581 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.465010.0991.02912.3
5.136.4610.1191.03813.7
4.485.1310.1061.01412.3
4.074.4810.1341.01512.2
3.784.0710.1891.01112.9
3.563.7810.2741.06213.1
3.383.5610.4141.06212.8
3.233.3810.5791.05210.7
3.113.2310.6411.0099.3
33.1110.7380.9777.2
ReflectionResolution: 2.45→50 Å / Num. obs: 21233 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 49.78 Å2 / Rmerge(I) obs: 0.116 / Χ2: 1.023 / Net I/av σ(I): 16.882 / Net I/σ(I): 6.7 / Num. measured all: 136611
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.45-2.544.80.99620570.99797.3
2.54-2.645.30.78821050.95898.8
2.64-2.766.20.65220871.05699.6
2.76-2.96.50.46221201.008100
2.9-3.097.10.31521131.002100
3.09-3.327.10.24221461.067100
3.32-3.666.80.16521071.032100
3.66-4.196.90.121451.022100
4.19-5.2870.06721611.058100
5.28-506.70.06621921.00299.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIXphenix.refine: 1.8_1069refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→45.088 Å / FOM work R set: 0.8037 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1051 4.95 %
Rwork0.204 20161 -
obs0.2055 21212 98.68 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.94 Å2 / Biso mean: 53.39 Å2 / Biso min: 27.46 Å2
Refinement stepCycle: final / Resolution: 2.45→45.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 20 13 2991
Biso mean--67.53 47.21 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033052
X-RAY DIFFRACTIONf_angle_d0.8444154
X-RAY DIFFRACTIONf_chiral_restr0.06497
X-RAY DIFFRACTIONf_plane_restr0.003506
X-RAY DIFFRACTIONf_dihedral_angle_d13.6721054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4274-2.53790.33171210.27692315243691
2.5379-2.67170.30271600.23742469262999
2.6717-2.8390.26511280.209925462674100
2.839-3.05820.24381240.19525192643100
3.0582-3.36580.26871100.202825922702100
3.3658-3.85270.2191270.195625372664100
3.8527-4.8530.19291310.19125832714100
4.853-45.09530.23651500.206226002750100

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