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- PDB-4lz6: Structure of MATE multidrug transporter DinF-BH -

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Basic information

Entry
Database: PDB / ID: 4lz6
TitleStructure of MATE multidrug transporter DinF-BH
ComponentsBH2163 protein
KeywordsTRANSPORT PROTEIN / multidrug transporter
Function / homologyMultidrug and toxic compound extrusion MepA-like / : / Multi antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / response to antibiotic / plasma membrane / Multidrug export protein MepA
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.2 Å
AuthorsLu, M. / Radchenko, M. / Symersky, J. / Nie, R. / Guo, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structural insights into H(+)-coupled multidrug extrusion by a MATE transporter
Authors: Lu, M. / Radchenko, M. / Symersky, J. / Nie, R. / Guo, Y.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Mar 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: BH2163 protein


Theoretical massNumber of molelcules
Total (without water)48,6151
Polymers48,6151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.759, 95.073, 101.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BH2163 protein


Mass: 48615.172 Da / Num. of mol.: 1 / Fragment: UNP residues 3-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KAX3

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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: 4.51 Å3/Da / Density % sol: 72.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: PEG, NaCl, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→60 Å / Num. obs: 14873 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.056
Reflection shellHighest resolution: 3.2 Å / Redundancy: 15 % / Mean I/σ(I) obs: 58.5 / Num. unique all: 14873 / Rsym value: 0.056 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.2→15 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.31 712 Random
Rwork0.29 --
obs0.3 14249 -
all-14500 -
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 0 0 3413
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg2
X-RAY DIFFRACTIONr_bond_refined_d0.01
LS refinement shellHighest resolution: 3.2 Å
RfactorNum. reflection% reflection
Rfree0.31 712 -
Rwork0.29 --
obs-14249 97 %

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