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- PDB-5yck: Crystal structure of a MATE family protein derived from Camelina ... -

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Basic information

Entry
Database: PDB / ID: 5yck
TitleCrystal structure of a MATE family protein derived from Camelina sativa at 2.3 angstrom
Componentsmulti drug efflux transporter
KeywordsTRANSPORT PROTEIN / membrane protein / multi drug resistance / transporter
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the plasma membrane / antiporter activity / xenobiotic transmembrane transporter activity / membrane
Similarity search - Function
Multidrug and toxic compound extrusion family, eukaryotic / Multi antimicrobial extrusion protein / MatE
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RUBIDIUM ION / Protein DETOXIFICATION
Similarity search - Component
Biological speciesCamelina sativa (false flax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsTanaka, Y. / Tsukazaki, T. / Iwaki, S.
CitationJournal: Structure / Year: 2017
Title: Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein
Authors: Tanaka, Y. / Iwaki, S. / Tsukazaki, T.
History
DepositionSep 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_database_related
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_database_related.content_type
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: multi drug efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6676
Polymers51,4271
Non-polymers1,2415
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-23 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.650, 69.240, 116.950
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 multi drug efflux transporter


Mass: 51426.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelina sativa (false flax) / Gene: false flax / Plasmid: pPic9k / Production host: Komagataella pastoris (fungus) / References: UniProt: R0G998*PLUS
#2: Chemical ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rb
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS USED THE NCBI Reference Sequence: XP_010514235.1.

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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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 7.1
Details: 33% PEG300, 200mM (NH4)2SO4, 100mM Tris, 100mM RbCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.623 Å / Num. obs: 21982 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 12.508 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.403 / Rrim(I) all: 0.418 / Χ2: 1.329 / Net I/σ(I): 6.48 / Num. measured all: 274945 / Scaling rejects: 227
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.4412.7252.4511.4235140.5542.54597.5
2.44-2.6112.5951.4322.1533100.7031.48798
2.61-2.8212.1770.982.9630560.8071.01996.8
2.82-3.0912.5390.6234.4528490.9060.64797.1
3.09-3.4512.8670.4156.6825530.9470.4398
3.45-3.9812.8470.26910.5222910.980.27997.7
3.98-4.8712.1440.21314.2819650.9820.22297.3
4.87-6.8911.8310.18613.3815430.9790.19496.1
6.89-45.62312.4330.11720.799010.9960.12294.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.65 Å45.63 Å
Translation6.65 Å45.63 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XSCALEdata scaling
PHASER2.5.3phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJJ

5xjj


Resolution: 2.3→45.623 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6
RfactorNum. reflection% reflection
Rfree0.2536 1999 9.12 %
Rwork0.2227 --
obs0.2256 21912 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.11 Å2 / Biso mean: 30.94 Å2 / Biso min: 14.55 Å2
Refinement stepCycle: final / Resolution: 2.3→45.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3453 0 77 84 3614
Biso mean--46.77 34.96 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023610
X-RAY DIFFRACTIONf_angle_d0.4444906
X-RAY DIFFRACTIONf_chiral_restr0.034583
X-RAY DIFFRACTIONf_plane_restr0.003594
X-RAY DIFFRACTIONf_dihedral_angle_d7.5612084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.35760.32041390.2691391153097
2.3576-2.42140.25421410.25051404154598
2.4214-2.49260.28721410.23371397153897
2.4926-2.57310.24261410.22531410155198
2.5731-2.6650.29631410.21971404154598
2.665-2.77170.22081410.21151406154797
2.7717-2.89780.21741410.20561400154196
2.8978-3.05060.26791390.2231395153498
3.0506-3.24170.24721440.22221427157198
3.2417-3.49190.26611430.2171432157598
3.4919-3.84310.26111450.21231440158598
3.8431-4.39880.24641450.22241441158698
4.3988-5.54050.2471450.23481449159497
5.5405-45.63150.23891530.21181517167096

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