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- PDB-3vvr: Crystal structure of MATE in complex with MaD5 -

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Basic information

Entry
Database: PDB / ID: 3vvr
TitleCrystal structure of MATE in complex with MaD5
Components
  • Putative uncharacterized protein
  • macrocyclic peptide
KeywordsTRANSPORT PROTEIN/INHIBITOR / MATE / multidrug transporter / macrocyclic peptide / TRANSPORT PROTEIN / 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: 3 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 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: macrocyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4445
Polymers50,3752
Non-polymers1,0703
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-16 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.521, 59.599, 68.335
Angle α, β, γ (deg.)90.000, 90.990, 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: Protein/peptide macrocyclic peptide / MaD5


Mass: 1098.272 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.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.2 Å3/Da / Density % sol: 61.6 % / Mosaicity: 1.003 °
Crystal growTemperature: 293 K / Method: lipdic cubic phase / pH: 7
Details: 30% PEG 400, 100mM HEPES-NaOH, 100mM NaSCN, pH 7.0, 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 MX225HE / Detector: CCD / Date: Oct 22, 2011
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: 3→50 Å / Num. all: 12863 / Num. obs: 12863 / % possible obs: 99.08 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.236 / Χ2: 1.559 / Net I/σ(I): 3.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.12.70.4217451.421188.3
3.1-3.172.80.3957870.939189.5
3.17-3.262.90.47620.964190.1
3.26-3.3630.3917640.966190.3
3.36-3.4630.3887851.119190.8
3.46-3.593.20.3597811.017191.8
3.59-3.733.30.3367931.09191.5
3.73-3.93.50.3158021.091193.5
3.9-4.113.80.2618131.13194.5
4.11-4.364.10.2148271.285194.4
4.36-4.73.80.1936791.276179.7
4.7-5.174.30.1788161.366193.9
5.17-5.923.90.2068391.467195.7
5.92-7.464.20.1828541.662196.9
7.46-504.90.0748891.788197.1
2.4081
1.9771
1.5541
1.7661
2.3631

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVN

3vvn


Resolution: 3→39.624 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7152 / SU ML: 1.05 / σ(F): 1.36 / Phase error: 34.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3087 1276 9.92 %RANDOM
Rwork0.2665 ---
all0.2707 12863 --
obs0.2707 12863 99.08 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.823 Å2 / ksol: 0.281 e/Å3
Displacement parametersBiso max: 129.38 Å2 / Biso mean: 59.388 Å2 / Biso min: 15.91 Å2
Baniso -1Baniso -2Baniso -3
1-21.4118 Å20 Å212.0168 Å2
2---13.508 Å2-0 Å2
3----7.9037 Å2
Refinement stepCycle: LAST / Resolution: 3→39.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 49 8 3217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033260
X-RAY DIFFRACTIONf_angle_d0.7264420
X-RAY DIFFRACTIONf_chiral_restr0.046548
X-RAY DIFFRACTIONf_plane_restr0.003541
X-RAY DIFFRACTIONf_dihedral_angle_d13.551085
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.12010.41121420.38031276141899
3.1201-3.26210.36951370.348412851422100
3.2621-3.4340.39041390.319312791418100
3.434-3.6490.32951420.28112791421100
3.649-3.93050.27961400.260812941434100
3.9305-4.32560.29151420.234112911433100
4.3256-4.95050.28381380.24961244138295
4.9505-6.23320.31511440.278413021446100
6.2332-39.62780.26751520.21781337148999
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)
10.84780.27371.13641.64370.18290.0862-0.0373-0.0622-0.0539-0.63780.05660.1984-0.2053-0.18640.01330.19380.02750.0560.225-0.02910.135234.49860.715123.8152
20.7984-1.03590.46682.2211-0.00890.4681-0.04320.0154-0.04230.1170.1856-0.228-0.08110.09530.02260.1733-0.02410.02470.0948-0.00660.141340.31041.533131.47
31.0365-0.12490.11570.24740.16820.331-0.2099-0.0503-0.0659-0.17880.09880.23150.0037-0.144-0.02730.2012-0.06890.02120.2815-0.03850.336424.3369-6.906316.5833
41.4273-1.2135-0.69041.38811.1010.8945-0.05740.2929-0.2494-0.2644-0.13450.1440.2083-0.5327-0.00040.3425-0.0661-0.16410.5877-0.02340.420316.2375-8.464614.9416
50.00640.0140.00360.05780.04350.00810.05310.02430.00540.15350.3169-0.19470.46010.0484-0.00121.43220.24590.23160.8910.31981.053428.7024-3.644828.2392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 4:126)A4 - 126
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 127:235)A127 - 235
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 236:340)A236 - 340
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 341:454)A341 - 454
5X-RAY DIFFRACTION5CHAIN BB0 - 11

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