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- PDB-6idp: Crystal structure of Vibrio cholerae MATE transporter VcmN in the... -

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Basic information

Entry
Database: PDB / ID: 6idp
TitleCrystal structure of Vibrio cholerae MATE transporter VcmN in the straight form
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: 2.205 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)54,29820
Polymers47,5241
Non-polymers6,77419
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19650 Å2
Unit cell
Length a, b, c (Å)62.225, 92.027, 101.302
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: 47523.531 Da / Num. of mol.: 1
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.: 19 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: PEG500DME, Tris-HCl, magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→46.014 Å / Num. obs: 29962 / % possible obs: 99.6 % / Redundancy: 7.005 % / Biso Wilson estimate: 34.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.167 / Χ2: 1.01 / Net I/σ(I): 10.51 / Num. measured all: 209892
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.21-2.345.691.2691.3726487475746550.5391.39797.9
2.34-2.57.2750.8632.3432803451045090.7970.93100
2.5-2.77.3710.5473.7830938419741970.8970.589100
2.7-2.967.3610.345.9128509387338730.9620.366100
2.96-3.37.3240.2248.9125891353535350.9810.241100
3.3-3.817.2910.11916.1722734311831180.9930.128100
3.81-4.667.1440.06826.6519109268026750.9980.07399.8
4.66-6.567.0750.06127.7315034212521250.9980.066100
6.56-46.0146.5780.035378387128212750.9990.03899.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.205→46.014 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.8
RfactorNum. reflection% reflection
Rfree0.2405 1999 6.68 %
Rwork0.198 --
obs0.2008 29907 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.73 Å2 / Biso mean: 47.1673 Å2 / Biso min: 19.55 Å2
Refinement stepCycle: final / Resolution: 2.205→46.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 195 89 3600
Biso mean--59.33 45.36 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033571
X-RAY DIFFRACTIONf_angle_d0.7824791
X-RAY DIFFRACTIONf_chiral_restr0.026565
X-RAY DIFFRACTIONf_plane_restr0.004567
X-RAY DIFFRACTIONf_dihedral_angle_d13.3061286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2051-2.26030.32911330.2991871200495
2.2603-2.32140.29771410.269319612102100
2.3214-2.38970.27931400.243919652105100
2.3897-2.46680.27551430.232719842127100
2.4668-2.5550.28071400.207619602100100
2.555-2.65730.21741420.190519762118100
2.6573-2.77820.22731430.1919842127100
2.7782-2.92470.2621420.186319902132100
2.9247-3.10790.22151420.187519862128100
3.1079-3.34770.23751430.186320072150100
3.3477-3.68450.2371450.180720162161100
3.6845-4.21740.24051440.18120102154100
4.2174-5.31220.22431470.191520512198100
5.3122-46.02350.22091540.199421472301100
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)
12.04361.2114-0.47123.4072-1.30581.96530.2183-0.3796-0.0280.7467-0.19140.0526-0.19840.0958-0.02510.3804-0.053-0.02530.2914-0.04630.28131.904-25.6109-27.1513
20.4671-0.1486-0.66541.20032.1463.8168-0.0945-0.037-0.05650.17130.0388-0.03530.22140.07640.0580.2649-0.0028-0.00730.21930.03570.328711.6534-7.4467-25.1892
30.7491-0.1561-1.27212.16712.16446.61630.1303-0.14130.16460.0020.2609-0.247-0.22770.725-0.36260.1827-0.0121-0.03980.294-0.00390.360921.9249-2.4762-26.4195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 225 )A4 - 225
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 393 )A226 - 393
3X-RAY DIFFRACTION3chain 'A' and (resid 394 through 441 )A394 - 441

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