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- PDB-4zp2: Crystal structure of E. coli multidrug transporter MdfA in comple... -

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Basic information

Entry
Database: PDB / ID: 4zp2
TitleCrystal structure of E. coli multidrug transporter MdfA in complex with n-dodecyl-N,N-dimethylamine-N-oxide
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
Multidrug transporter MdfA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 16, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)42,9203
Polymers42,4621
Non-polymers4592
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint3 kcal/mol
Surface area16960 Å2
Unit cell
Length a, b, c (Å)94.086, 64.085, 101.253
Angle α, β, γ (deg.)90.000, 104.190, 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: 42461.629 Da / Num. of mol.: 1 / Fragment: UNP residues 9-400 / Mutation: Q123R
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-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 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: 2.2→50 Å / Num. obs: 29691 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 40.18 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.09 / Net I/av σ(I): 15.368 / Net I/σ(I): 6.6 / Num. measured all: 255213
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.2-2.288.229601.243100
2.28-2.378.729460.9931000.994
2.37-2.488.829491.0241000.783
2.48-2.618.829351.0761000.577
2.61-2.778.729581.2321000.45
2.77-2.998.829571.0921000.264
2.99-3.298.829431.0251000.177
3.29-3.768.630041.0511000.12
3.76-4.748.229851.0651000.081
4.74-508.330541.1199.90.058

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXphenix.refine: 1.8_1069refinement
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.438 Å / FOM work R set: 0.8249 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 1473 4.97 %
Rwork0.2063 28168 -
obs0.2076 29641 99.12 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.01 Å2 / Biso mean: 51.58 Å2 / Biso min: 27.48 Å2
Refinement stepCycle: final / Resolution: 2.2→38.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 32 18 3020
Biso mean--67.33 46.46 -
Num. residues----392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053074
X-RAY DIFFRACTIONf_angle_d1.0444177
X-RAY DIFFRACTIONf_chiral_restr0.076497
X-RAY DIFFRACTIONf_plane_restr0.004505
X-RAY DIFFRACTIONf_dihedral_angle_d14.4321080
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1985-2.26950.32161310.31412317244891
2.2695-2.35060.32041210.277425862707100
2.3506-2.44470.29361360.250725542690100
2.4447-2.55590.26231390.228425562695100
2.5559-2.69070.26191490.219725672716100
2.6907-2.85920.2361400.193825712711100
2.8592-3.07990.23311310.189925732704100
3.0799-3.38960.23411120.200726122724100
3.3896-3.87970.20071280.196325942722100
3.8797-4.88650.19431330.194526012734100
4.8865-38.4440.23461530.195226372790100

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