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- PDB-7dqk: A nicotine MATE transporter, Nicotiana tabacum MATE2 (NtMATE2) -

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Basic information

Entry
Database: PDB / ID: 7dqk
TitleA nicotine MATE transporter, Nicotiana tabacum MATE2 (NtMATE2)
ComponentsProtein DETOXIFICATION
KeywordsTRANSPORT PROTEIN / multidrug efflux transporter
Function / homology
Function and homology information


antiporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / membrane => GO:0016020 / membrane
Similarity search - Function
Multi antimicrobial extrusion protein / MatE
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Protein DETOXIFICATION
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTanaka, Y. / Tsukazaki, T. / Sasaki, A. / Iwaki, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Febs Lett. / Year: 2021
Title: Crystal structures of a nicotine MATE transporter provide insight into its mechanism of substrate transport.
Authors: Tanaka, Y. / Iwaki, S. / Sasaki, A. / Tsukazaki, T.
History
DepositionDec 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein DETOXIFICATION
B: Protein DETOXIFICATION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8467
Polymers111,1582
Non-polymers6885
Water27015
1
A: Protein DETOXIFICATION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1374
Polymers55,5791
Non-polymers5583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-8 kcal/mol
Surface area20670 Å2
MethodPISA
2
B: Protein DETOXIFICATION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7093
Polymers55,5791
Non-polymers1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-5 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.000, 89.370, 228.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 55579.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: NtMATE2, LOC107807968 / Plasmid: pPic9K / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: A3KDM5

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Non-polymers , 5 types, 20 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: monoolein (NU-CHEK-PREP), PEG 300 (Sigma-Aldrich), NH4H2PO4, HEPES-Na, 2.5 mM nicotine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 16478 / % possible obs: 99.67 % / Redundancy: 34.4 % / Biso Wilson estimate: 96.72 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.66
Reflection shellResolution: 3.5→3.625 Å / Mean I/σ(I) obs: 1.18 / Num. unique obs: 1625 / CC1/2: 0.621
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography data reductionCrystal hits: 94

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Processing

Software
NameVersionClassification
PHENIX1.19rc6_4061refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YCK

5yck


Resolution: 3.5→48.2 Å / SU ML: 0.5671 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.2171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3113 1644 9.99 %
Rwork0.2586 14806 -
obs0.2637 16450 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.85 Å2
Refinement stepCycle: LAST / Resolution: 3.5→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7327 0 43 15 7385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00177541
X-RAY DIFFRACTIONf_angle_d0.43810253
X-RAY DIFFRACTIONf_chiral_restr0.0331198
X-RAY DIFFRACTIONf_plane_restr0.00341246
X-RAY DIFFRACTIONf_dihedral_angle_d4.40251042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.60.42581360.37451226X-RAY DIFFRACTION100
3.6-3.720.3471330.32151202X-RAY DIFFRACTION100
3.72-3.850.39881340.30481212X-RAY DIFFRACTION99.93
3.85-4.010.33931340.28581209X-RAY DIFFRACTION99.93
4.01-4.190.33961330.27511205X-RAY DIFFRACTION99.93
4.19-4.410.29731360.25921226X-RAY DIFFRACTION100
4.41-4.690.32191360.26351224X-RAY DIFFRACTION99.13
4.69-5.050.29681360.24991217X-RAY DIFFRACTION99.56
5.05-5.550.30821390.26191239X-RAY DIFFRACTION99.64
5.55-6.360.35641380.28441243X-RAY DIFFRACTION99.78
6.36-80.28171400.24561262X-RAY DIFFRACTION100
8-48.20.25571490.20211341X-RAY DIFFRACTION99.14
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.511003894050.2713422011122.252398008810.286639593850.04512126050643.27719221426-0.0911952782367-0.345818628440.6084784165170.313106719723-0.138310062014-0.5230850105140.7316727884880.537469914340.3527390500271.509643141210.44219991662-0.2670853925281.23583006296-0.2475352188641.13605934071-4.14175731298-52.5683562577-17.2266330417
21.208674830890.110592671524-0.01236029462821.296145755750.1112895931311.24279427089-0.0961491398099-0.043338552405-0.0387452301289-0.111764219672-0.0769658994148-0.2550619611050.4702795717610.1037993455560.08468048043750.7218131981150.06733034545170.05526335701710.639317832462-0.01064684798580.636306864306-23.8412571398-42.7563106211-26.4663334075
32.40518587878-0.128155234624-0.1561470613250.451891702064-0.9284795440182.004196729230.03995974101790.1535314168570.05087653520430.2468568649390.06945230334940.0058976469670.1704549236630.173992402966-0.1284249683430.9046080422250.0427674487542-0.04480141619490.628961524194-0.07579971068160.706778979028-0.942187096725-38.661389304-30.0698936901
42.03679676952-0.4364542004330.4524851740011.59083215555-0.03600399857370.231834059937-0.236568167796-0.3000823349020.2458582582140.1634533009620.273703627289-0.234611430185-0.201202454019-0.521825146858-0.06474373246470.900317643212-0.0877297359917-0.01240027493310.9552749973540.02311225784390.72201539990814.1597586633-18.7444019947-20.0721574291
50.651652642220.0531609340213-0.4397504661171.14080893597-0.07843603396311.945815918290.01718665138120.03350218923830.0970124413906-0.006649560330380.1052812215140.0735183316887-0.393507261049-0.131401314472-0.1277311896490.785421457907-0.00909718321780.01569348449290.8506607708890.01793428079020.65296309897315.7760808573-4.92557300716-33.2841932335
60.9448869308840.525407054975-0.959832180011.21268939884-1.135918405531.36400839280.152421645325-0.1744110699431.031501803180.304448134865-0.551141865994-0.308487408438-0.06852124952860.848137221146-0.04044674093150.5802252286470.1119244771-0.06049338192550.9439348212510.1212472937910.81623031231331.500581433-8.13110126082-26.1872194393
72.938605213080.5762601813151.325332766941.59936237072-0.3334567764153.0783671060.280424660687-0.03688583353840.06433533409970.01843036677510.0665370303674-0.289816642342-0.5095237137440.03579194226420.03040980006010.6593412143830.09480032490550.03757980841470.7007878518590.04654091283720.64890311956233.3887826164-9.58677990614-29.0747547868
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 18 through 78 )AA18 - 781 - 61
22chain 'A' and (resid 79 through 267 )AA79 - 26762 - 250
33chain 'A' and (resid 268 through 493 )AA268 - 493251 - 476
44chain 'B' and (resid 15 through 78 )BB15 - 781 - 64
55chain 'B' and (resid 79 through 404 )BB79 - 40465 - 390
66chain 'B' and (resid 405 through 430 )BB405 - 430391 - 416
77chain 'B' and (resid 431 through 493 )BB431 - 493417 - 479

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