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- PDB-6zgt: Crystal structure of a MFS transporter with bound 2-naphthoic aci... -

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Basic information

Entry
Database: PDB / ID: 6zgt
TitleCrystal structure of a MFS transporter with bound 2-naphthoic acid at 2.39 Angstroem resolution
ComponentsL-lactate transporter
KeywordsMEMBRANE PROTEIN / L-lactate transporter / monocarboxylate transporter / SLC16 family
Function / homologysymporter activity / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / plasma membrane / naphthalene-2-carboxylic acid / L-lactate transporter
Function and homology information
Biological speciesSyntrophobacter fumaroxidans MPOB (syntrophic propionate-oxidizing bacterium DSM 10017)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 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)89,9444
Polymers89,5992
Non-polymers3442
Water1086
1
A: L-lactate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9722
Polymers44,8001
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lactate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9722
Polymers44,8001
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.534, 199.623, 61.934
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-FIV / naphthalene-2-carboxylic acid / 2-naphthoic acid / 2-Naphthoic acid


Mass: 172.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.54 Å3/Da / Density % sol: 65.23 % / Mosaicity: 0.1 °
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: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→49.66 Å / Num. obs: 62970 / % possible obs: 100 % / Redundancy: 59.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.019 / Rrim(I) all: 0.14 / Net I/σ(I): 28.9 / Num. measured all: 3733279 / Scaling rejects: 34612
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) all% possible allRmerge(I) obs
2.23-2.355290440.25110.24375.19499.9
7.05-49.6647.721990.9970.0130.09599.70.094

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.77 Å49.66 Å
Translation3.77 Å49.66 Å

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Processing

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

6g9x


Resolution: 2.23→19.962 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 1995 4.74 %
Rwork0.2153 40079 -
obs0.2164 42074 67.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.31 Å2 / Biso mean: 101.2827 Å2 / Biso min: 36.28 Å2
Refinement stepCycle: final / Resolution: 2.23→19.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 26 6 5822
Biso mean--71.77 73.33 -
Num. residues----768
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3210X-RAY DIFFRACTION7.234TORSIONAL
12B3210X-RAY DIFFRACTION7.234TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2301-2.28580.4745200.32833909
2.2858-2.34750.4225270.283656013
2.3475-2.41650.3586410.272380719
2.4165-2.49430.3196630.2693127030
2.4943-2.58330.2771890.262178742
2.5833-2.68650.26911190.2375238757
2.6865-2.80840.28921530.2376309173
2.8084-2.95610.2421880.2226377989
2.9561-3.14060.25022120.22854238100
3.1406-3.3820.23992120.21574275100
3.382-3.72040.23022140.19884288100
3.7204-4.25420.20542150.19024315100
4.2542-5.34280.252160.21024357100
5.3428-19.9620.24212260.22824535100
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)
13.1145-1.2933-0.0156.25381.82653.10280.20730.26220.3948-1.4537-0.37530.4729-0.7852-0.35820.1580.60.1304-0.1110.3387-0.00020.2816-9.12730.59210.5741
26.21090.8313-1.21715.2170.43644.5105-0.1722-0.5883-0.65640.03060.0619-1.29110.54120.99690.17040.33440.083-0.00480.6726-0.06220.629830.431223.679227.6563
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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