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- PDB-6lgz: Crystal structure of a cysteine-pair mutant (P10C-S291C) of a bac... -

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Basic information

Entry
Database: PDB / ID: 6lgz
TitleCrystal structure of a cysteine-pair mutant (P10C-S291C) of a bacterial bile acid transporter in an inward-facing state complexed with sulfate
ComponentsTransporter, sodium/bile acid symporter family
KeywordsTRANSPORT PROTEIN / Bile acid transporter / ASBT / NTCP / SLC10
Function / homologyBile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / membrane / 2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Ketopantoate/pantoate/pantothenate transporter PanS
Function and homology information
Biological speciesYersinia frederiksenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.428 Å
AuthorsWang, X. / Lyu, Y. / Ji, Y. / Sun, Z. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770783 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Substrate binding in the bile acid transporter ASBT Yf from Yersinia frederiksenii.
Authors: Wang, X. / Lyu, Y. / Ji, Y. / Sun, Z. / Zhou, X.
History
DepositionDec 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transporter, sodium/bile acid symporter family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9106
Polymers33,3881
Non-polymers1,5225
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-21 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.578, 44.416, 71.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-618-

HOH

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Components

#1: Protein Transporter, sodium/bile acid symporter family


Mass: 33387.898 Da / Num. of mol.: 1 / Mutation: P10C, S291C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia frederiksenii (bacteria) / Gene: NCTC11470_02445 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A380PV03
#2: Chemical
ChemComp-A6L / 2,3-dihydroxypropyl (9Z)-octadec-9-enoate / monoolein


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 7.5
Details: 0.2 M (NH4)2SO4, 0.1 M Tris-HCl pH 7.5, 32% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.428→39.704 Å / Num. obs: 10859 / % possible obs: 96.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 39.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.046 / Rrim(I) all: 0.112 / Net I/σ(I): 10.5 / Num. measured all: 56163
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.428-2.474.80.61426895630.8290.30.6862.598.3
6.581-39.7044.70.03926955690.9990.0190.04328.289.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LGV

6lgv


Resolution: 2.428→39.704 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 528 4.87 %
Rwork0.2346 10311 -
obs0.2363 10839 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.47 Å2 / Biso mean: 45.9897 Å2 / Biso min: 24.38 Å2
Refinement stepCycle: final / Resolution: 2.428→39.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 0 105 28 2406
Biso mean--67.8 44.29 -
Num. residues----304
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.428-2.67210.30041250.2619256498
2.6721-3.05870.33521380.2501257198
3.0587-3.85310.27831410.2335255397
3.8531-39.7040.23291240.2236262394
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)
12.1345-0.0361-0.5171.2426-0.18172.2192-0.0752-0.25680.3857-0.00110.1263-0.0418-0.2928-0.2240.06610.47810.0518-0.03990.3295-0.07190.331820.5532-7.6003-6.5239
23.79070.1042-0.58021.88240.13662.67760.07710.2296-0.46450.0162-0.25550.0622-0.1282-0.25710.18640.36140.0262-0.02350.3063-0.09340.314321.5802-26.0836-19.9128
31.4510.73081.24110.39670.41582.9649-0.24230.19320.7496-0.1892-0.08350.002-0.56370.44410.34130.59320.0224-0.0410.3478-0.05080.513632.0282-16.9677-12.1302
41.12250.1034-0.29711.1093-0.04781.2792-0.0225-0.08670.0490.0679-0.0148-0.0766-0.1135-0.18540.04220.35090.0194-0.00470.3326-0.0360.253321.57-17.9188-15.6846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 48 )A-1 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 101 )A49 - 101
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 118 )A102 - 118
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 302 )A119 - 302

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