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- PDB-6zgr: Crystal structure of a MFS transporter with bound 1-hydroxynaphth... -

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Basic information

Entry
Database: PDB / ID: 6zgr
TitleCrystal structure of a MFS transporter with bound 1-hydroxynaphthalene-2-carboxylic acid at 2.67 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
1-hydroxynaphthalene-2-carboxylic 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: 2.46 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)89,9764
Polymers89,5992
Non-polymers3762
Water362
1
A: L-lactate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9882
Polymers44,8001
Non-polymers1881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-lactate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9882
Polymers44,8001
Non-polymers1881
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.553, 199.572, 62.468
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 11 through 160 or resid 167 through 191 or resid 218 through 407))
21(chain B and (resid 11 through 160 or resid 167 through 407))

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
11TRPTRPILEILE(chain A and (resid 11 through 160 or resid 167 through 191 or resid 218 through 407))AA11 - 16011 - 160
12TRPTRPPROPRO(chain A and (resid 11 through 160 or resid 167 through 191 or resid 218 through 407))AA167 - 191167 - 191
13ASPASPPROPRO(chain A and (resid 11 through 160 or resid 167 through 191 or resid 218 through 407))AA218 - 407218 - 407
21TRPTRPILEILE(chain B and (resid 11 through 160 or resid 167 through 407))BB11 - 16011 - 160
22TRPTRPPROPRO(chain B and (resid 11 through 160 or resid 167 through 407))BB167 - 407167 - 407

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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-1HN / 1-hydroxynaphthalene-2-carboxylic acid


Mass: 188.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.6 Å3/Da / Density % sol: 65.85 % / Mosaicity: 0.11 °
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: Sep 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→47.14 Å / Num. obs: 47962 / % possible obs: 100 % / Redundancy: 47.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.022 / Rrim(I) all: 0.145 / Net I/σ(I): 22 / Num. measured all: 2295711 / Scaling rejects: 48405
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) all% possible allRmerge(I) obs
2.46-2.5949.368960.19639.476281.73599.9
7.78-47.1435.616820.9990.010.06299.60.061

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.77 Å47.14 Å
Translation3.77 Å47.14 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: 2.46→14.983 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1519 5 %
Rwork0.2209 28858 -
obs0.2226 30377 63.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 226.37 Å2 / Biso mean: 102.4572 Å2 / Biso min: 31.44 Å2
Refinement stepCycle: final / Resolution: 2.46→14.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5749 0 28 2 5779
Biso mean--80.37 73.17 -
Num. residues----763
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3162X-RAY DIFFRACTION7.72TORSIONAL
12B3162X-RAY DIFFRACTION7.72TORSIONAL
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 (%)
2.4605-2.53950.3542300.31155558514
2.5395-2.62980.3521370.296371575218
2.6298-2.73450.32500.280393898823
2.7345-2.85810.2695650.26921236130130
2.8581-3.00770.29081000.2661919201947
3.0077-3.19440.3021550.26632953310872
3.1944-3.43830.25591990.24323766396592
3.4383-3.77930.23672170.220641264343100
3.7793-4.31470.25722170.201941234340100
4.3147-5.39350.24662210.211941824403100
5.3935-14.98290.25482280.220243454573100
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)
16.12931.496-2.08365.67490.55974.5348-0.2101-0.6864-0.7553-0.2285-0.0221-1.43220.58851.0130.01910.3230.12050.08610.6019-0.00220.614133.690423.581490.4551
21.8843-1.8342-0.57245.20422.32573.72090.24320.21620.2893-1.327-0.49160.4295-0.9029-0.4360.23930.64040.1571-0.17790.3421-0.05110.411394.085130.667674.0602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 11 through 407)B11 - 407
2X-RAY DIFFRACTION2(chain 'A' and resid 7 through 420)A7 - 420

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