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

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Basic information

Entry
Database: PDB / ID: 6kkk
TitleCrystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB, in the inward open conformation (H115A mutant)
ComponentsSugar efflux transporter
KeywordsTRANSPORT PROTEIN / MFS Transporter
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
Sugar efflux transporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 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 26, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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: Sugar efflux transporter
B: Sugar efflux transporter
C: Sugar efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,1916
Polymers136,2723
Non-polymers9193
Water00
1
A: Sugar efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7302
Polymers45,4241
Non-polymers3061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint5 kcal/mol
Surface area15820 Å2
MethodPISA
2
B: Sugar efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7302
Polymers45,4241
Non-polymers3061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint4 kcal/mol
Surface area16150 Å2
MethodPISA
3
C: Sugar efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7302
Polymers45,4241
Non-polymers3061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.618, 61.822, 122.463
Angle α, β, γ (deg.)90.000, 93.420, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 133 or (resid 134...
21(chain B and (resid 8 through 11 or (resid 12...
31(chain C and (resid 8 through 11 or (resid 12...

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
11ARGARGGLYGLY(chain A and (resid 8 through 133 or (resid 134...AA8 - 13335 - 160
12LYSLYSALAALA(chain A and (resid 8 through 133 or (resid 134...AA134 - 138161 - 165
13ARGARGGLUGLU(chain A and (resid 8 through 133 or (resid 134...AA8 - 39235 - 419
14ARGARGGLUGLU(chain A and (resid 8 through 133 or (resid 134...AA8 - 39235 - 419
15ARGARGGLUGLU(chain A and (resid 8 through 133 or (resid 134...AA8 - 39235 - 419
16ARGARGGLUGLU(chain A and (resid 8 through 133 or (resid 134...AA8 - 39235 - 419
21ARGARGALAALA(chain B and (resid 8 through 11 or (resid 12...BB8 - 1135 - 38
22TRPTRPTRPTRP(chain B and (resid 8 through 11 or (resid 12...BB1239
23ARGARGGLUGLU(chain B and (resid 8 through 11 or (resid 12...BB8 - 39235 - 419
24ARGARGGLUGLU(chain B and (resid 8 through 11 or (resid 12...BB8 - 39235 - 419
25ARGARGGLUGLU(chain B and (resid 8 through 11 or (resid 12...BB8 - 39235 - 419
31ARGARGALAALA(chain C and (resid 8 through 11 or (resid 12...CC8 - 1135 - 38
32TRPTRPTRPTRP(chain C and (resid 8 through 11 or (resid 12...CC1239
33ARGARGGLUGLU(chain C and (resid 8 through 11 or (resid 12...CC8 - 39235 - 419
34ARGARGGLUGLU(chain C and (resid 8 through 11 or (resid 12...CC8 - 39235 - 419
35ARGARGGLUGLU(chain C and (resid 8 through 11 or (resid 12...CC8 - 39235 - 419

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Components

#1: Protein Sugar efflux transporter


Mass: 45423.926 Da / Num. of mol.: 3 / Mutation: H115A
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.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC 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: 3.63 Å3/Da / Density % sol: 66.09 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30% PEG 400, 0.1 M Sodium chloride, 0.1 M Lithium sulfate, 0.1 M Sodium citrate tribasic dihydrate pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.485→50 Å / Num. obs: 25106 / % possible obs: 98.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.098 / Rrim(I) all: 0.21 / Χ2: 0.487 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.633.70.60424660.450.3520.7030.33697.9
3.63-3.773.60.54524440.4680.3260.6390.33798
3.77-3.9440.4724800.6730.2650.5430.37698.8
3.94-4.154.40.39225080.7960.210.4470.39299.2
4.15-4.414.50.30325010.8990.1590.3440.4399.2
4.41-4.754.40.23125100.9270.1230.2630.50399.5
4.75-5.234.80.22425040.9410.1150.2540.45499.2
5.23-5.984.70.25425090.9290.130.2860.41698.9
5.98-7.534.80.15125540.9810.0780.1710.45999.1
7.53-505.20.05826300.9950.0290.0650.95699.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→47.176 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.48
RfactorNum. reflection% reflection
Rfree0.2674 1987 7.94 %
Rwork0.2311 --
obs0.234 25024 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.21 Å2 / Biso mean: 70.0898 Å2 / Biso min: 29.21 Å2
Refinement stepCycle: final / Resolution: 3.5→47.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8430 0 63 0 8493
Biso mean--71.5 --
Num. residues----1143
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3432X-RAY DIFFRACTION6.736TORSIONAL
12B3432X-RAY DIFFRACTION6.736TORSIONAL
13C3432X-RAY DIFFRACTION6.736TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5-3.57160.38221390.3213147991
3.5716-3.66820.32781270.3045162697
3.6682-3.77610.3111450.2821158497
3.7761-3.89790.32281480.2766165998
3.8979-4.03710.31561320.2525162999
4.0371-4.19870.32651420.2571166999
4.1987-4.38960.29211480.2186165099
4.3896-4.62090.24891410.19151646100
4.6209-4.91010.2521420.1878165899
4.9101-5.28880.24881400.19481671100
5.2888-5.82010.27471460.2134165099
5.8201-6.66030.29781470.2356167699
6.6603-8.38360.19291390.2087169099
8.3836-47.1760.21591510.2283175099

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