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- PDB-3wbn: Crystal structure of MATE in complex with MaL6 -

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Basic information

Entry
Database: PDB / ID: 3wbn
TitleCrystal structure of MATE in complex with MaL6
Components
  • MaL6
  • Putative uncharacterized protein
KeywordsTRANSPORT PROTEIN/INHIBITOR / MATE / multidrug transporter / TRANSPORT PROTEIN-INHIBITOR complex
Function / homology: / : / Multi antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / plasma membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / MATE family efflux transporter
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsTanaka, Y. / Ishitani, R. / Nureki, O.
CitationJournal: Nature / Year: 2013
Title: Structural basis for the drug extrusion mechanism by a MATE multidrug transporter.
Authors: Tanaka, Y. / Hipolito, C.J. / Matunara, A.D. / Ito, K. / Kuroda, T. / Higuchi, T. / Kato, T. / Hattori, M. / Kumazaki, K. / Kato, H.E. / Tsukazaki, T. / Ishitani, R. / Suga, H. / Nureki, O.
History
DepositionMay 20, 2013Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 12, 2013ID: 3VVQ
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: MaL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3647
Polymers51,5812
Non-polymers1,7835
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-3 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.728, 59.828, 68.034
Angle α, β, γ (deg.)90.000, 91.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

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Components

#1: Protein Putative uncharacterized protein


Mass: 49276.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: JCM 8422 / Gene: PF0708 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q8U2X0
#2: Protein/peptide MaL6


Mass: 2304.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Selected by the RaPID system protocol
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 59.17 % / Mosaicity: 0.225 °
Crystal growTemperature: 293 K / Method: lipdic cubic phase / pH: 8
Details: 30% PEG 400, 100mM Tris-HCl, 20mM CaCl2, 100mM NaSCN, pH 8.0, lipdic cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.91 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 16, 2012
RadiationMonochromator: liquid nitrogen cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22898 / % possible obs: 95.3 % / Redundancy: 15 % / Rmerge(I) obs: 0.238 / Χ2: 1.803 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.4-2.4413.68261.335168.9
2.44-2.4913.99131.309177
2.49-2.5313.910621.344190.8
2.53-2.5915.212071.356199.2
2.59-2.6415.511631.353198.7
2.64-2.715.512021.42199.10.926
2.7-2.7715.511411.438199.10.855
2.77-2.8515.512271.452199.40.748
2.85-2.9315.511771.491199.10.623
2.93-3.0215.511851.536199.30.547
3.02-3.1315.411991.617199.30.462
3.13-3.2615.411801.681199.30.383
3.26-3.4115.411881.744199.30.311
3.41-3.5815.411881.865199.50.239
3.58-3.8115.312102.001199.70.192
3.81-4.115.311942.436199.60.143
4.1-4.5212.910772.858188.80.114
4.52-5.1714.310842.781190.10.105
5.17-6.511512192.441199.80.13
6.51-5014.412562.598199.40.059

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVN

3vvn


Resolution: 2.45→33.626 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8417 / SU ML: 0.2 / σ(F): 1.35 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1932 8.77 %
Rwork0.1865 --
obs0.1903 22034 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.23 Å2 / Biso mean: 32.7519 Å2 / Biso min: 2.77 Å2
Refinement stepCycle: LAST / Resolution: 2.45→33.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 62 61 3616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043621
X-RAY DIFFRACTIONf_angle_d0.7744897
X-RAY DIFFRACTIONf_chiral_restr0.049595
X-RAY DIFFRACTIONf_plane_restr0.003591
X-RAY DIFFRACTIONf_dihedral_angle_d13.2411267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.51130.27741170.22311171128879
2.5113-2.57910.2691390.2011402154197
2.5791-2.6550.2391340.19091472160699
2.655-2.74070.23921380.17791458159699
2.7407-2.83860.27331420.18381472161499
2.8386-2.95220.23861340.18221452158699
2.9522-3.08640.24431400.18691475161599
3.0864-3.2490.26851430.18741476161999
3.249-3.45240.22551420.18591456159899
3.4524-3.71860.23111370.177214951632100
3.7186-4.09230.18481470.172214741621100
4.0923-4.68310.22661240.18791253137784
4.6831-5.8950.22131420.210215181660100
5.895-33.6290.18821530.17541528168199
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)
10.37570.07460.18080.5217-0.18490.9859-0.00810.0494-0.05190.02870.0108-0.06550.0115-0.08380.00290.2323-0.0245-0.00010.1543-0.00950.2202340.5013-3.85227.8807
20.77850.1027-0.25460.2178-0.13330.6597-0.01370.0526-0.0613-0.09890.02460.02390.1328-0.0343-0.00690.2328-0.0093-0.01150.2729-0.03880.2421323.4123-12.912716.7588
33.08680.5404-1.28912.97771.15331.20460.1215-0.0908-0.1631-0.17930.12720.1182-0.2254-0.0831-0.16350.336-0.03830.06740.4422-0.01090.336314.8842-1.267435.869
45.30981.05272.34712.1584-0.13565.7202-0.12220.07680.3391-0.4460.16460.5326-0.4352-0.6773-0.08210.20490.0898-0.01650.4419-0.04830.4328311.8974-0.507430.2758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 5:235 )
2X-RAY DIFFRACTION2chain A and (resid 236:454 )
3X-RAY DIFFRACTION3chain B and (resid 0:10 )
4X-RAY DIFFRACTION4chain B and (resid 11:18 )

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