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- PDB-5y50: Crystal structure of eukaryotic MATE transporter AtDTX14 -

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Basic information

Entry
Database: PDB / ID: 5y50
TitleCrystal structure of eukaryotic MATE transporter AtDTX14
ComponentsProtein DETOXIFICATION 14
KeywordsMEMBRANE PROTEIN / alpha helical
Function / homology
Function and homology information


plant-type vacuole / xenobiotic detoxification by transmembrane export across the plasma membrane / antiporter activity / xenobiotic transport / xenobiotic transmembrane transporter activity / membrane
Similarity search - Function
Multidrug and toxic compound extrusion family, eukaryotic / Multi antimicrobial extrusion protein / MatE
Similarity search - Domain/homology
Protein DETOXIFICATION 14
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
Model detailsa receptor
AuthorsMiyauchi, H. / Kusakizako, T. / Nishizawa, T. / Ishitani, R. / Nureki, O.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for xenobiotic extrusion by eukaryotic MATE transporter
Authors: Miyauchi, H. / Moriyama, S. / Kusakizako, T. / Kumazaki, K. / Nakane, T. / Yamashita, K. / Hirata, K. / Dohmae, N. / Nishizawa, T. / Ito, K. / Miyaji, T. / Moriyama, Y. / Ishitani, R. / Nureki, O.
History
DepositionAug 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 2023Group: 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: Protein DETOXIFICATION 14


Theoretical massNumber of molelcules
Total (without water)49,5441
Polymers49,5441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17970 Å2
Unit cell
Length a, b, c (Å)52.800, 86.780, 116.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein DETOXIFICATION 14 / AtDTX14 / Multidrug and toxic compound extrusion protein 14 / MATE protein 14


Mass: 49544.004 Da / Num. of mol.: 1 / Fragment: UNP residues 20-473 / Mutation: P36A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DTX14, At1g71140, F23N20.13 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9C994

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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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: Na-citrate, MgSO4, NaK-tartrate-tetrahydrate, PEG550MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.345 Å / Num. obs: 16880 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 28.488 % / Biso Wilson estimate: 47.81 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.576 / Rrim(I) all: 0.587 / Χ2: 1.197 / Net I/σ(I): 7.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.7628.4826.7120.927670.6096.833100
2.76-2.9528.9783.0961.5725280.8083.151100
2.95-3.1829.2261.8282.4823290.8741.86100
3.18-3.4929.2441.0514.2322570.9341.069100
3.49-3.929.020.5398.5919960.9740.549100
3.9-4.527.8360.34513.8316010.9840.35190.1
4.5-5.5127.5610.24418.1114570.9940.24994.8
5.51-7.7827.8170.20919.2212170.9960.213100
7.78-48.34525.0540.1328.457280.9970.13399.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MKT

3mkt


Resolution: 2.6→48.345 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.87
RfactorNum. reflection% reflection
Rfree0.2759 842 5.01 %
Rwork0.2238 --
obs0.2266 16815 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.88 Å2 / Biso mean: 52.1982 Å2 / Biso min: 25.08 Å2
Refinement stepCycle: final / Resolution: 2.6→48.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 0 0 3362
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083432
X-RAY DIFFRACTIONf_angle_d0.9434657
X-RAY DIFFRACTIONf_chiral_restr0.047558
X-RAY DIFFRACTIONf_plane_restr0.006566
X-RAY DIFFRACTIONf_dihedral_angle_d17.0472000
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.76290.35341400.302126602800100
2.7629-2.97620.3531390.271926582797100
2.9762-3.27560.32591410.2526642805100
3.2756-3.74950.2711420.226826842826100
3.7495-4.72330.25491290.20032454258391
4.7233-48.3530.23721510.199228533004100

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