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- PDB-6hcl: Crystal structure of a MFS transporter with Ligand at 2.69 Angstr... -

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Basic information

Entry
Database: PDB / ID: 6hcl
TitleCrystal structure of a MFS transporter with Ligand at 2.69 Angstroem resolution
ComponentsMajor facilitator superfamily MFS_1
KeywordsMEMBRANE PROTEIN / MFS transporter
Function / homologyMajor facilitator superfamily / Major Facilitator Superfamily / symporter activity / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / plasma membrane / (2S)-2-HYDROXYPROPANOIC ACID / L-lactate transporter
Function and homology information
Biological speciesSyntrophobacter fumaroxidans MPOB (syntrophic propionate-oxidizing bacterium DSM 10017)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKalbermatter, D. / Bosshart, P. / Bonetti, S. / Fotiadis, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2019
Title: Mechanistic basis of L-lactate transport in the SLC16 solute carrier family.
Authors: Bosshart, P.D. / Kalbermatter, D. / Bonetti, S. / Fotiadis, D.
History
DepositionAug 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / software / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _software.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major facilitator superfamily MFS_1
B: Major facilitator superfamily MFS_1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1766
Polymers89,5992
Non-polymers5774
Water0
1
A: Major facilitator superfamily MFS_1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1963
Polymers44,8001
Non-polymers3962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Major facilitator superfamily MFS_1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9803
Polymers44,8001
Non-polymers1802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.423, 200.016, 63.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Major facilitator superfamily MFS_1


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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0LNN5
#2: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID / Lactic acid


Mass: 90.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H6O3
#3: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 4.23 Å3/Da / Density % sol: 70.94 %
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
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.52 Å / Num. obs: 30961 / % possible obs: 94.4 % / Redundancy: 55.9 % / Biso Wilson estimate: 94.8 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.118 / Net I/σ(I): 40.8
Reflection shellResolution: 2.5→2.68 Å / Redundancy: 57.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1341 / CC1/2: 0.59 / Rpim(I) all: 0.9 / Rrim(I) all: 5.1 / % possible all: 88.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSJan 26, 2018 (BUILT 20180302)data reduction
autoPROC1.0.5 (20170920)data scaling
PHASER2.8.1phasing
Coot0.8.9.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G9X

6g9x


Resolution: 2.5→24.826 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.98
RfactorNum. reflection% reflection
Rfree0.2593 1545 5 %
Rwork0.239 --
obs0.24 30902 66.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5732 0 39 0 5771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075940
X-RAY DIFFRACTIONf_angle_d0.9118076
X-RAY DIFFRACTIONf_dihedral_angle_d12.2273302
X-RAY DIFFRACTIONf_chiral_restr0.05902
X-RAY DIFFRACTIONf_plane_restr0.007981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5003-2.58090.4338250.421489X-RAY DIFFRACTION12
2.5809-2.67310.4952380.3415716X-RAY DIFFRACTION18
2.6731-2.77990.3562560.32291055X-RAY DIFFRACTION27
2.7799-2.90630.316830.2851583X-RAY DIFFRACTION40
2.9063-3.05920.30041240.28662344X-RAY DIFFRACTION59
3.0592-3.25050.30341610.27813071X-RAY DIFFRACTION77
3.2505-3.50090.25872000.24393791X-RAY DIFFRACTION95
3.5009-3.8520.24982090.22913982X-RAY DIFFRACTION100
3.852-4.40670.22842120.21184026X-RAY DIFFRACTION100
4.4067-5.54180.29492150.23474066X-RAY DIFFRACTION100
5.5418-24.82760.24372220.24514234X-RAY DIFFRACTION100
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)
12.84080.3159-0.2172.4824-0.3112.66810.15450.69070.0194-1.7612-0.6010.6813-0.4102-0.67540.08381.36380.4076-0.29610.5086-0.0470.5528-13.715233.16171.8472
21.8021-0.61690.05973.75010.98113.07360.0864-0.19180.4293-0.5849-0.02550.0765-0.4636-0.23570.00460.30140.0511-0.0070.3337-0.06480.354-5.451628.754719.5947
33.05710.27990.38573.2648-0.0523.00870.17770.10690.2612-0.282-0.1767-2.52140.39821.1974-0.0261.04910.46940.22851.39560.06011.330938.338423.467825.3335
42.279-0.38090.33541.5106-0.23991.7182-0.19540.0693-0.0014-0.12180.127-1.0670.2381.1589-0.20120.46640.65280.58551.9189-0.03471.752746.1521.210420.494
53.1013-0.2836-0.95573.04620.02224.29550.1718-0.9632-0.07970.43560.2174-1.58270.88291.19820.06451.23870.1775-0.11041.69860.49831.669136.231120.264636.3525
61.6169-1.0672-0.14244.93261.20853.96050.2370.8412-0.0822-0.34550.6783-1.5159-0.55110.99770.53580.57490.24880.09382.39680.17572.223850.164828.184628.18
72.90740.39710.2511.63560.06073.9952-0.409-0.3985-0.8260.21470.219-1.62391.33270.4221-0.08881.10340.13960.07910.8763-0.02061.116722.930116.925427.8936
83.99220.00510.54493.75840.49253.58920.0125-0.31430.31810.08470.0039-0.26120.39830.27820.00630.5638-0.03660.05470.749-0.09090.513219.959826.231130.6273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 187 )
2X-RAY DIFFRACTION2chain 'A' and (resid 188 through 420 )
3X-RAY DIFFRACTION3chain 'B' and (resid 11 through 74 )
4X-RAY DIFFRACTION4chain 'B' and (resid 75 through 109 )
5X-RAY DIFFRACTION5chain 'B' and (resid 110 through 158 )
6X-RAY DIFFRACTION6chain 'B' and (resid 159 through 187 )
7X-RAY DIFFRACTION7chain 'B' and (resid 188 through 258 )
8X-RAY DIFFRACTION8chain 'B' and (resid 259 through 407 )

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