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- PDB-6g9x: Crystal structure of a MFS transporter at 2.54 Angstroem resolution -

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Basic information

Entry
Database: PDB / ID: 6g9x
TitleCrystal structure of a MFS transporter at 2.54 Angstroem resolution
ComponentsMajor facilitator superfamily MFS_1
KeywordsMEMBRANE PROTEIN / MFS transporter
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
: / 2-sulfanylbenzoic acid / L-lactate transporter
Similarity search - Component
Biological speciesSyntrophobacter fumaroxidans
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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
DepositionApr 11, 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_conn / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)94,39223
Polymers89,5992
Non-polymers4,79221
Water362
1
A: Major facilitator superfamily MFS_1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,51613
Polymers44,8001
Non-polymers2,71612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Major facilitator superfamily MFS_1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,87610
Polymers44,8001
Non-polymers2,0769
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.765, 200.539, 64.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein / Sugars , 2 types, 8 molecules AB

#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 (strain DSM 10017 / MPOB) (syntrophic propionate-oxidizing bacterium DSM 10017)
Gene: Sfum_3364 / Production host: Escherichia coli (E. coli) / References: UniProt: A0LNN5
#5: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 6
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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Non-polymers , 4 types, 17 molecules

#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-JKE / 2-sulfanylbenzoic acid / Thiosalicylic acid


Mass: 154.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2S
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 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: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→53.26 Å / Num. obs: 34625 / % possible obs: 94 % / Redundancy: 12.9 % / Biso Wilson estimate: 69.31 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Net I/σ(I): 19.9
Reflection shellResolution: 2.3→2.54 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1731 / CC1/2: 0.594 / Rpim(I) all: 0.7 / Rrim(I) all: 1.7 / % possible all: 87.1

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Processing

Software
NameVersionClassification
XDSJun 1, 2017 (BUILT 20170615data reduction
autoPROC1.0.5 (20170920)data scaling
CRANK22.0.153phasing
BUCCANEER1.6.4model building
Coot0.8.9model building
PHENIX1.13_2998refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→24.79 Å / SU ML: 0.2826 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.7672
RfactorNum. reflection% reflection
Rfree0.2541 1996 5.78 %
Rwork0.2175 --
obs0.2196 34558 55.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 80.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5757 0 173 2 5932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00886090
X-RAY DIFFRACTIONf_angle_d1.15568265
X-RAY DIFFRACTIONf_chiral_restr0.0597928
X-RAY DIFFRACTIONf_plane_restr0.0076986
X-RAY DIFFRACTIONf_dihedral_angle_d12.46883374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.4191170.3923277X-RAY DIFFRACTION6.72
2.36-2.420.3839250.3502396X-RAY DIFFRACTION9.67
2.42-2.50.3793320.3513536X-RAY DIFFRACTION12.92
2.5-2.580.3743450.311725X-RAY DIFFRACTION17.62
2.58-2.670.4014570.3027951X-RAY DIFFRACTION22.97
2.67-2.770.2712720.28991170X-RAY DIFFRACTION28.22
2.77-2.90.3264950.26881539X-RAY DIFFRACTION37.19
2.9-3.050.30111520.26082478X-RAY DIFFRACTION59.21
3.05-3.240.28972010.25183283X-RAY DIFFRACTION79
3.24-3.490.2592500.22024074X-RAY DIFFRACTION97.65
3.49-3.840.22592570.24198X-RAY DIFFRACTION99.87
3.84-4.40.22992580.18744220X-RAY DIFFRACTION100
4.4-5.530.25972620.18484271X-RAY DIFFRACTION100
5.53-24.790.25252730.24364444X-RAY DIFFRACTION99.64
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)
13.09141630411-1.78367170956-0.03297330913746.179998738091.195594245462.928340065380.2362429522470.4095309656170.243589572215-1.35340330469-0.5752571213530.3074111475-0.763721474666-0.455627729960.2106882885160.4415140457330.174846214138-0.1581797340710.299707727271-0.06288485630210.12607995689195.885034244330.260934296645.6501047272
26.196060506090.27828042823-0.8886763663316.455602948711.203215435633.127902751190.185892510092-0.614821054774-0.329657412681-0.131038671029-0.0829754602311-1.308723553560.1391772783450.910531918608-0.008781275087910.270402227688-0.007553573682380.0215487190590.5481095047210.03242306918210.410313744399135.60759753123.346998141561.394984587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 420)
2X-RAY DIFFRACTION2(chain 'B' and resid 11 through 410)

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