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- PDB-3vvo: Crystal structure of MATE in the bent conformation -

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Basic information

Entry
Database: PDB / ID: 3vvo
TitleCrystal structure of MATE in the bent conformation
ComponentsPutative uncharacterized protein
KeywordsTRANSPORT PROTEIN / MATE / multidrug transporter
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: 2.504 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. / Maturana, A.D. / Ito, K. / Kuroda, T. / Higuchi, T. / Katoh, T. / Kato, H.E. / Hattori, M. / Kumazaki, K. / Tsukazaki, T. / Ishitani, R. / Suga, H. / Nureki, O.
History
DepositionJul 27, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,84211
Polymers49,2761
Non-polymers3,56510
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.893, 58.835, 71.491
Angle α, β, γ (deg.)90.000, 93.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative uncharacterized protein / Archaeal-type transporter


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: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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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: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 293 K / Method: lipdic cubic phase / pH: 6.5
Details: 32% PEG 400, 50mM MES-NaOH, 20mM CaCl2, 100mM NaSCN, pH 6.5, lipdic cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 27, 2012
RadiationMonochromator: liquid nitrogen cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.504→31.663 Å / Num. all: 21175 / Num. obs: 21175 / % possible obs: 95.89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.41 Å2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 15.2 / Num. unique all: 1098 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.504→31.663 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8065 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 2010 9.49 %RANDOM
Rwork0.2065 ---
all0.2113 21175 --
obs0.2113 21175 95.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.78 Å2 / Biso mean: 46.9953 Å2 / Biso min: 18.29 Å2
Refinement stepCycle: LAST / Resolution: 2.504→31.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 136 41 3460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063469
X-RAY DIFFRACTIONf_angle_d0.8794660
X-RAY DIFFRACTIONf_chiral_restr0.056566
X-RAY DIFFRACTIONf_plane_restr0.003556
X-RAY DIFFRACTIONf_dihedral_angle_d14.8041248
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 (%)
2.5043-2.56690.33341390.28271279141890
2.5669-2.63620.32991480.24871400154899
2.6362-2.71380.31221420.24271408155099
2.7138-2.80130.2921550.23181395155099
2.8013-2.90140.2841480.23041385153399
2.9014-3.01750.28551380.21851426156499
3.0175-3.15470.26061530.21651397155099
3.1547-3.32080.26041480.21421415156399
3.3208-3.52860.29281450.2051418156399
3.5286-3.80070.2731480.192214121560100
3.8007-4.18240.24721490.176214471596100
4.1824-4.78580.2346940.19786095460
4.7858-6.02280.24421480.211214361584100
6.0228-31.66530.18461550.18361487164299
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)
11.9306-1.4061-3.70291.23511.62719.00240.0461-0.07140.00090.0375-0.0028-0.04880.15370.00160.14090.3162-0.06690.01260.2166-0.03980.3493333.2714-4.924168.0098
20.569-0.30320.80821.62790.41031.1820.0460.05320.1814-0.1190.06990.0547-0.2359-0.1463-0.0870.30030.00540.0070.16360.04370.2363328.120711.427169.2336
31.02270.3622-0.78361.1912-0.41972.9190.01220.04190.0715-0.253-0.0028-0.0249-0.20660.08680.10620.3126-0.0214-0.00750.17540.00270.2407336.9526.5327175.9716
47.77185.5306-6.93425.1939-4.87317.96860.3043-0.19460.03210.2308-0.21780.14-0.1982-0.2944-0.02930.3641-0.02280.01720.2876-0.02780.23317.54248.1482162.3594
54.5023-3.1869-4.92482.9243.26085.42360.37750.02010.5603-0.21010.20260.1625-0.0063-0.6811-0.37360.32260.04520.03930.58450.0350.3518308.3424-6.4753173.7034
67.21263.2626-5.10873.2964-2.98127.3009-0.38650.0068-0.393-0.5226-0.0248-0.22010.59910.10070.37350.25130.0489-0.00470.16630.00110.1822326.3041-10.1156153.9193
72.2395-0.16880.26313.0672-1.28050.5357-0.18160.0816-0.1349-0.05180.22070.0584-0.05-0.42-0.06540.4107-0.0153-0.00430.3686-0.03490.263310.8437-6.1344162.6175
84.0392-0.152-3.2111.6099-0.31214.23740.31310.20190.364-0.24180.10070.0519-0.0601-0.1286-0.12890.31340.0015-0.02560.3994-0.0290.2006313.8331-4.2167150.1876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 4:49 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 50:130 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 131:235 )
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 236:269 )
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 270:290 )
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 291:340 )
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 341:420 )
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 421:457 )

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