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- PDB-6e9n: E. coli D-galactonate:proton symporter in the inward open form -

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Basic information

Entry
Database: PDB / ID: 6e9n
TitleE. coli D-galactonate:proton symporter in the inward open form
ComponentsD-galactonate transport
KeywordsMEMBRANE PROTEIN / MFS Transporter / SLC17 / organic anion transporter
Function / homologyMajor facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / transmembrane transporter activity / plasma membrane / D-gluconic acid / D-galactonate transport
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.915 Å
AuthorsLeano, J.B. / Edwards, R.H. / Stroud, R.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH50712 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM24485 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS089713 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM024485-37S1 United States
CitationJournal: Plos Biol. / Year: 2019
Title: Structures suggest a mechanism for energy coupling by a family of organic anion transporters.
Authors: Leano, J.B. / Batarni, S. / Eriksen, J. / Juge, N. / Pak, J.E. / Kimura-Someya, T. / Robles-Colmenares, Y. / Moriyama, Y. / Stroud, R.M. / Edwards, R.H.
History
DepositionAug 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: D-galactonate transport
B: D-galactonate transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7358
Polymers101,0072
Non-polymers1,7286
Water0
1
A: D-galactonate transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3124
Polymers50,5031
Non-polymers8093
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-galactonate transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4234
Polymers50,5031
Non-polymers9193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.700, 107.630, 103.210
Angle α, β, γ (deg.)90.00, 108.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D-galactonate transport / D-galactonate transporter


Mass: 50503.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dgoT, BN17_36391, HMPREF3040_00185 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: J7QAK3
#2: Sugar ChemComp-GCO / D-gluconic acid / GLUCONIC ACID / Gluconic acid


Type: D-saccharide / Mass: 196.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O7
#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.: 5
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: 4.14 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.35 / Details: 100mM sodium acetate pH 5.35, 39% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 24356 / % possible obs: 70 % / Redundancy: 1.9 % / CC1/2: 0.75 / Net I/σ(I): 6.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 512 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PW4

1pw4


Resolution: 2.915→48.277 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.95
RfactorNum. reflection% reflection
Rfree0.2968 1255 5.94 %
Rwork0.243 --
obs0.2461 21115 60.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.915→48.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 118 0 6472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036657
X-RAY DIFFRACTIONf_angle_d0.5619048
X-RAY DIFFRACTIONf_dihedral_angle_d11.2163702
X-RAY DIFFRACTIONf_chiral_restr0.0361041
X-RAY DIFFRACTIONf_plane_restr0.0041079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9146-3.03130.5847120.3753143X-RAY DIFFRACTION4
3.0313-3.16920.4202300.3386431X-RAY DIFFRACTION12
3.1692-3.33630.393480.3266814X-RAY DIFFRACTION22
3.3363-3.54530.3927850.31931380X-RAY DIFFRACTION38
3.5453-3.81890.36311560.28582600X-RAY DIFFRACTION71
3.8189-4.2030.30842230.24453532X-RAY DIFFRACTION97
4.203-4.81070.26632320.20783642X-RAY DIFFRACTION100
4.8107-6.05910.28652360.253641X-RAY DIFFRACTION100
6.0591-48.2840.27052330.22913677X-RAY DIFFRACTION99

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