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- PDB-4tko: Structure of the periplasmic adaptor protein EmrA -

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Basic information

Entry
Database: PDB / ID: 4tko
TitleStructure of the periplasmic adaptor protein EmrA
ComponentsEmrA
KeywordsMEMBRANE PROTEIN / MFS / Multidrug resistance / periplasmic adaptor
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the plasma membrane / xenobiotic transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Efflux pump membrane protein / Membrane fusion protein, biotin-lipoyl like domain / Biotin-lipoyl like / Efflux pump adaptor protein, beta barrel domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Biotin_lipoyl_2 domain-containing protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsHinchliffe, P. / Greene, N.P. / Paterson, N.G. / Crow, A. / Hughes, C. / Koronakis, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust093011/Z/10/Z United Kingdom
CitationJournal: Febs Lett. / Year: 2014
Title: Structure of the periplasmic adaptor protein from a major facilitator superfamily (MFS) multidrug efflux pump.
Authors: Hinchliffe, P. / Greene, N.P. / Paterson, N.G. / Crow, A. / Hughes, C. / Koronakis, V.
History
DepositionMay 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: EmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4674
Polymers41,3221
Non-polymers1443
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.366, 81.366, 541.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein EmrA


Mass: 41322.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1060 / Production host: Escherichia coli (E. coli) / References: UniProt: O67159
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 5.42 Å3/Da / Density % sol: 77.32 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MES pH 6.5, 100mM MgCl2, 10% isopropanol, 8% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.03836 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03836 Å / Relative weight: 1
ReflectionResolution: 2.85→29.67 Å / Num. obs: 22191 / % possible obs: 99.98 % / Redundancy: 11.9 % / Net I/σ(I): 9.7
Reflection shellResolution: 2.85→3 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.85→29.67 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1080 4.88 %
Rwork0.2079 --
obs0.2098 22150 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 9 6 2669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082692
X-RAY DIFFRACTIONf_angle_d0.9873596
X-RAY DIFFRACTIONf_dihedral_angle_d17.381080
X-RAY DIFFRACTIONf_chiral_restr0.038413
X-RAY DIFFRACTIONf_plane_restr0.003446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.97970.29071190.22672576X-RAY DIFFRACTION100
2.9797-3.13660.27921330.24072599X-RAY DIFFRACTION100
3.1366-3.33290.31431510.2322522X-RAY DIFFRACTION100
3.3329-3.58990.28841190.2312627X-RAY DIFFRACTION100
3.5899-3.95040.24111410.2052607X-RAY DIFFRACTION100
3.9504-4.52030.21441570.18822607X-RAY DIFFRACTION100
4.5203-5.68850.22031200.19552675X-RAY DIFFRACTION100
5.6885-29.67190.24231400.20272857X-RAY DIFFRACTION100

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