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- PDB-5c6n: protein A -

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Basic information

Entry
Database: PDB / ID: 5c6n
Titleprotein A
ComponentsBH2163 protein
KeywordsTRANSPORT PROTEIN / protein A
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 / Resolution: 3 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: Nat Commun / Year: 2015
Title: Structural basis for the blockade of MATE multidrug efflux pumps.
Authors: Radchenko, M. / Symersky, J. / Nie, R. / Lu, M.
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 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)50,5651
Polymers50,5651
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)89.678, 93.418, 101.786
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: 50565.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria)
Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / 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

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Sample preparation

CrystalDensity Matthews: 4.22 Å3/Da / Density % sol: 70.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 15805 / % possible obs: 90 % / Redundancy: 9 % / Net I/σ(I): 20.2

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementResolution: 3→20 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3 --
Rwork0.28 --
obs-14860 90 %
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 0 0 3413

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