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- PDB-6kki: Crystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB,... -

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Basic information

Entry
Database: PDB / ID: 6kki
TitleCrystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB, in the inward-occluded conformation
ComponentsSugar efflux transporter
KeywordsPROTEIN TRANSPORT / Transporter protein / MFS
Function / homology
Function and homology information


transmembrane transporter activity / carbohydrate transmembrane transporter activity / transmembrane transport / plasma membrane
Similarity search - Function
Sugar efflux transporter, putative / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
1-methylethyl 1-thio-beta-D-galactopyranoside / Sugar efflux transporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.064 Å
AuthorsXiao, Q.J. / Deng, D.
Funding support China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)YFA052700 China
National Science Foundation (China)JQ007 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Visualizing the nonlinear changes of a drug-proton antiporter from inward-open to occluded state.
Authors: Xiao, Q. / Sun, B. / Zhou, Y. / Wang, C. / Guo, L. / He, J. / Deng, D.
History
DepositionJul 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugar efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3424
Polymers45,4911
Non-polymers8513
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.778, 84.698, 88.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sugar efflux transporter / MFS family protein


Mass: 45490.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: sotB, ydeA, b1528, JW1521 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31122
#2: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-IPT / 1-methylethyl 1-thio-beta-D-galactopyranoside / ISOPROPYL-1-BETA-D-THIOGALACTOSIDE / 1-(ISOPROPYLTHIO)-BETA-GALACTOPYRANSIDE / 1-methylethyl 1-thio-beta-D-galactoside / 1-methylethyl 1-thio-D-galactoside / 1-methylethyl 1-thio-galactoside


Type: D-saccharide / Mass: 238.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18O5S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
isopropyl-1-b-D-thiogalactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 5.6 / Details: 11% PEG 3350, 0.02 M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. obs: 10188 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 99.06 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.046 / Rrim(I) all: 0.112 / Χ2: 0.773 / Net I/σ(I): 4.8 / Num. measured all: 54555
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.05-3.164.60.5979860.530.3060.6730.29499.4
3.16-3.294.60.52510090.6490.2660.590.32299.4
3.29-3.434.50.3759780.8480.1910.4230.39699.6
3.43-3.625.10.310070.9160.1440.3340.48699.9
3.62-3.845.60.22810180.940.1040.2510.56100
3.84-4.145.80.16510000.980.0730.1810.85199.7
4.14-4.555.60.12310110.9870.0560.1361.04499.9
4.55-5.216.10.10310320.9910.0440.1121.11399.6
5.21-6.555.80.110390.990.0440.1091.06199.7
6.55-305.80.06611080.9960.030.0731.1499.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.064→27.36 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 29.85
RfactorNum. reflection% reflection
Rfree0.2707 990 9.75 %
Rwork0.2383 --
obs0.2412 10152 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 179.5 Å2 / Biso mean: 91.3341 Å2 / Biso min: 51.97 Å2
Refinement stepCycle: final / Resolution: 3.064→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 57 0 2788
Biso mean--104.01 --
Num. residues----366
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0642-3.22560.40931220.3558122194
3.2256-3.42730.31591440.3091296100
3.4273-3.69130.29971490.24291298100
3.6913-4.06170.24651410.20981298100
4.0617-4.6470.23761410.19311317100
4.647-5.84530.23971460.2371336100
5.8453-27.360.27711470.2404139699

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