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- PDB-6zgu: Crystal structure of a MFS transporter with bound 3-(2-methylphen... -

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Basic information

Entry
Database: PDB / ID: 6zgu
TitleCrystal structure of a MFS transporter with bound 3-(2-methylphenyl)propanoic acid at 2.41 Angstroem resolution
ComponentsL-lactate transporter
KeywordsMEMBRANE PROTEIN / L-lactate transporter / monocarboxylate transporter / SLC16 family
Function / homology
Function and homology information


symporter activity / plasma membrane
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
3-(2-methylphenyl)propanoic acid / L-lactate transporter
Similarity search - Component
Biological speciesSyntrophobacter fumaroxidans MPOB (syntrophic propionate-oxidizing bacterium DSM 10017)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å
AuthorsKalbermatter, D. / Bosshart, P. / Bonetti, S. / Fotiadis, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_184980 Switzerland
CitationJournal: Commun Chem / Year: 2021
Title: The making of a potent L-lactate transport inhibitor
Authors: Bosshart, P.D. / Kalbermatter, D. / Bonetti, S. / Fotiadis, D.
History
DepositionJun 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate transporter
B: L-lactate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9284
Polymers89,5992
Non-polymers3282
Water1448
1
A: L-lactate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9642
Polymers44,8001
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lactate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9642
Polymers44,8001
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.048, 199.703, 61.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 13 through 160 or resid 166 through 191 or resid 217 through 406))
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROILEILE(chain A and (resid 13 through 160 or resid 166 through 191 or resid 217 through 406))AA13 - 16013 - 160
12GLYGLYPROPRO(chain A and (resid 13 through 160 or resid 166 through 191 or resid 217 through 406))AA166 - 191166 - 191
13ARGARGPROPRO(chain A and (resid 13 through 160 or resid 166 through 191 or resid 217 through 406))AA217 - 406217 - 406
21PROPROPROPROchain BBB13 - 40613 - 406

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Components

#1: Protein L-lactate transporter / SfMCT


Mass: 44799.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophobacter fumaroxidans MPOB (syntrophic propionate-oxidizing bacterium DSM 10017)
Gene: Sfum_3364 / Plasmid: pZUDF21-rbs-3C-10His / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0LNN5
#2: Chemical ChemComp-02Q / 3-(2-methylphenyl)propanoic acid


Mass: 164.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.5 Å3/Da / Density % sol: 64.89 % / Mosaicity: 0.09 °
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: zinc bromide, HEPES, jeffamine ED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→49.44 Å / Num. obs: 66703 / % possible obs: 100 % / Redundancy: 32.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.031 / Rrim(I) all: 0.164 / Net I/σ(I): 18.9 / Num. measured all: 2143898 / Scaling rejects: 99709
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) all% possible allRmerge(I) obs
2.18-2.334.896240.1515.26431.4399.9
6.89-49.4417.723160.9990.0170.07899.70.076

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.77 Å49.44 Å

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHASER2.8.2phasing
PHENIX1.14_3228refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G9X

6g9x


Resolution: 2.18→14.968 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1988 4.82 %
Rwork0.2155 39235 -
obs0.2169 41223 62.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217.31 Å2 / Biso mean: 97.0232 Å2 / Biso min: 31.3 Å2
Refinement stepCycle: final / Resolution: 2.18→14.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 24 8 5822
Biso mean--73.56 66.71 -
Num. residues----768
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3160X-RAY DIFFRACTION6.8TORSIONAL
12B3160X-RAY DIFFRACTION6.8TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1801-2.23440.3981210.31014219
2.2344-2.29460.3049270.298651612
2.2946-2.36190.2813320.291764114
2.3619-2.43780.3571450.291289020
2.4378-2.52450.3012690.2929135130
2.5245-2.62510.3362930.2848185141
2.6251-2.74390.27591350.269266460
2.7439-2.88760.27351800.2522354779
2.8876-3.0670.25162230.247439497
3.067-3.30150.2962290.23654510100
3.3015-3.62940.24042290.20854536100
3.6294-4.14490.23572300.19824539100
4.1449-5.18570.2342340.20314615100
5.1857-14.9680.23142410.21174760100
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)
12.062-1.4133-0.17775.95372.41882.98480.23190.25230.3868-1.6105-0.36290.2152-0.9698-0.33650.11840.68580.1346-0.07130.34180.00190.2986-9.196730.643710.5378
25.30140.8661-1.03355.05180.99084.0512-0.2017-0.3822-0.71720.04830.1748-1.17560.60070.97060.15180.26240.10380.02410.6078-0.09870.609530.459923.675527.3024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 420)A7 - 420
2X-RAY DIFFRACTION2(chain 'B' and resid 13 through 406)B13 - 406

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