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- PDB-6ids: Crystal structure of Vibrio cholerae MATE transporter VcmN D35N mutant -

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Basic information

Entry
Database: PDB / ID: 6ids
TitleCrystal structure of Vibrio cholerae MATE transporter VcmN D35N mutant
ComponentsMATE family efflux transporter
KeywordsTRANSPORT PROTEIN / MATE multidrug transporter
Function / homology(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.79 Å
AuthorsKusakizako, T. / Claxton, D.P. / Tanaka, Y. / Maturana, A.D. / Kuroda, T. / Ishitani, R. / Mchaourab, H.S. / Nureki, O.
CitationJournal: Structure / Year: 2019
Title: Structural Basis of H+-Dependent Conformational Change in a Bacterial MATE Transporter.
Authors: Kusakizako, T. / Claxton, D.P. / Tanaka, Y. / Maturana, A.D. / Kuroda, T. / Ishitani, R. / Mchaourab, H.S. / Nureki, O.
History
DepositionSep 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MATE family efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5924
Polymers47,5231
Non-polymers1,0703
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19000 Å2
Unit cell
Length a, b, c (Å)62.468, 90.149, 102.257
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MATE family efflux transporter / VcmN


Mass: 47522.547 Da / Num. of mol.: 1 / Mutation: D35N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CGT79_05080 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2A1YWE9
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: PEG300, sodium citrate, ammonium fluoride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.79→102.26 Å / Num. obs: 14931 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 35.64 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.279 / Rpim(I) all: 0.123 / Rrim(I) all: 0.306 / Net I/σ(I): 5 / Num. measured all: 91363 / Scaling rejects: 402
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.79-2.9460.9241242420690.5670.4171.0172.596.1
8.82-102.265.20.11128765550.9770.0540.1257.699.9

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
PHASERphasing
RefinementResolution: 2.79→67.623 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 1486 9.99 %
Rwork0.2089 13393 -
obs0.2134 14879 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.95 Å2 / Biso mean: 32.9866 Å2 / Biso min: 5.21 Å2
Refinement stepCycle: final / Resolution: 2.79→67.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 30 13 3350
Biso mean--37.18 33.25 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033413
X-RAY DIFFRACTIONf_angle_d0.784646
X-RAY DIFFRACTIONf_chiral_restr0.023564
X-RAY DIFFRACTIONf_plane_restr0.005560
X-RAY DIFFRACTIONf_dihedral_angle_d14.1321171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7905-2.88060.31911290.24031169129896
2.8806-2.98350.28561310.226511871318100
2.9835-3.1030.29441340.222612021336100
3.103-3.24420.26381340.209312031337100
3.2442-3.41520.25411340.2112011335100
3.4152-3.62920.22921330.200112001333100
3.6292-3.90940.22141360.188412251361100
3.9094-4.30270.26031340.191212141348100
4.3027-4.92520.28051360.213612261362100
4.9252-6.20460.23561390.228212471386100
6.2046-67.64240.22341460.201513191465100

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