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- PDB-3vvn: Crystal structure of MATE in the straight conformation -

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Basic information

Entry
Database: PDB / ID: 3vvn
TitleCrystal structure of MATE in the straight 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 / SAD / Resolution: 2.398 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 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,55513
Polymers49,2761
Non-polymers4,27812
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.889, 60.100, 68.127
Angle α, β, γ (deg.)90.000, 90.270, 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.: 12 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.24 Å3/Da / Density % sol: 62.02 % / Mosaicity: 0.406 °
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: 0.979, 0.900, 0.910
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 21, 2011 / Details: mirrors
RadiationMonochromator: liquid nitrogen cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.91
30.911
ReflectionResolution: 2.398→50 Å / Num. all: 24440 / Num. obs: 24440 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.116 / Χ2: 0.897 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.443.70.3711740.482194.7
2.44-2.494.10.36711920.47198.8
2.49-2.534.30.36412420.513197.9
2.53-2.594.50.33412040.538198.9
2.59-2.644.60.34712100.554198.5
2.64-2.74.80.31112460.582199
2.7-2.7750.29312280.616199.7
2.77-2.8550.2812300.669199.3
2.85-2.935.20.25412200.665199.5
2.93-3.025.30.23712470.749199.6
3.02-3.135.40.20612280.789199.2
3.13-3.265.60.19112440.841100
3.26-3.415.70.16412300.926199.7
3.41-3.5860.13512341.006199.5
3.58-3.816.20.1112631.056199.8
3.81-4.16.30.08612301.19199.7
4.1-4.526.10.07611551.499192.1
4.52-5.176.20.07111031.408187.3
5.17-6.516.40.08612671.146199.9
6.51-506.70.04312931.216199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.398→43.331 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.859 / SU ML: 0.67 / σ(F): 0.08 / Phase error: 21.87 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1990 8.15 %RANDOM
Rwork0.2064 ---
all0.209 24429 --
obs0.209 24429 97.82 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.036 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 121.91 Å2 / Biso mean: 37.8429 Å2 / Biso min: 5.71 Å2
Baniso -1Baniso -2Baniso -3
1-3.5636 Å2-0 Å25.7831 Å2
2--0.6044 Å20 Å2
3----4.168 Å2
Refinement stepCycle: LAST / Resolution: 2.398→43.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 136 30 3458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033472
X-RAY DIFFRACTIONf_angle_d0.7534658
X-RAY DIFFRACTIONf_chiral_restr0.05566
X-RAY DIFFRACTIONf_plane_restr0.004554
X-RAY DIFFRACTIONf_dihedral_angle_d16.8331247
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 (%)
2.3975-2.45750.33831370.27211501163892
2.4575-2.52390.29931420.25421605174798
2.5239-2.59820.27281450.2381597174299
2.5982-2.6820.25231380.21661584172299
2.682-2.77790.23131410.20271623176499
2.7779-2.88910.23591470.19861617176499
2.8891-3.02050.22231410.185216301771100
3.0205-3.17970.20831430.17951622176599
3.1797-3.37890.22821490.182316331782100
3.3789-3.63960.21861450.17721629177499
3.6396-4.00570.21571450.191216561801100
4.0057-4.58470.22641280.19621439156788
4.5847-5.77410.23841440.22081602174697
5.7741-43.33840.23891450.22681701184699
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)
10.33960.03690.53641.79580.12350.8657-0.01860.0167-0.0233-0.0802-0.0242-0.0527-0.07810.08810.02560.15670.0103-0.0116-0.03870.01030.0844-36.93893.1798-27.5872
22.1074-0.636-0.74281.48290.34451.359-0.03320.0168-0.05510.0709-0.0398-0.26810.03740.25460.06160.0878-0.0229-0.01640.09590.04050.1317-19.0942-5.5816-16.5164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 4:235)A4 - 235
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 236:454)A236 - 454

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