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- PDB-6fhz: Inward-facing conformation of a multidrug resistance MATE family ... -

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Basic information

Entry
Database: PDB / ID: 6fhz
TitleInward-facing conformation of a multidrug resistance MATE family transporter of the MOP superfamily.
ComponentsPutative MOP flippase
KeywordsMEMBRANE PROTEIN / MOP flippase
Function / homology: / Multi antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / plasma membrane / MATE family efflux transporter
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZakrzewska, S. / Safarian, S. / Michel, H.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation Germany
Max Planck Society Germany
Cluster of Excellence for Macromolecular Complexes807 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Inward-facing conformation of a multidrug resistance MATE family transporter.
Authors: Zakrzewska, S. / Mehdipour, A.R. / Malviya, V.N. / Nonaka, T. / Koepke, J. / Muenke, C. / Hausner, W. / Hummer, G. / Safarian, S. / Michel, H.
History
DepositionJan 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jun 12, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 26, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Putative MOP flippase


Theoretical massNumber of molelcules
Total (without water)47,0301
Polymers47,0301
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.120, 134.310, 69.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative MOP flippase


Mass: 47029.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: PF0708 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U2X0

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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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 5
Details: 30% PEG 600, 100 mM Na3C6H5O7-C6H8O7, 100 mM NaCl, 100 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→43.7 Å / Num. obs: 12731 / % possible obs: 99.8 % / Redundancy: 8.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.082 / Rrim(I) all: 0.238 / Net I/σ(I): 8.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1263 / CC1/2: 0.296 / Rpim(I) all: 0.749 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MLB

4mlb


Resolution: 2.8→19.803 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.15
RfactorNum. reflection% reflection
Rfree0.274 612 4.83 %
Rwork0.2285 --
obs0.2306 12676 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.7 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 0 0 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013324
X-RAY DIFFRACTIONf_angle_d0.364517
X-RAY DIFFRACTIONf_dihedral_angle_d15.7141938
X-RAY DIFFRACTIONf_chiral_restr0.034556
X-RAY DIFFRACTIONf_plane_restr0.003555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.08090.36261410.31982984X-RAY DIFFRACTION100
3.0809-3.52450.31521660.2832960X-RAY DIFFRACTION100
3.5245-4.43230.29921540.21123012X-RAY DIFFRACTION100
4.4323-19.80330.22331510.20343108X-RAY DIFFRACTION99

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