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

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Basic information

Entry
Database: PDB / ID: 6lgy
TitleCrystal structure of a cysteine-pair mutant (P10C-S291C) of a bacterial bile acid transporter in an inward-facing state complexed with glycine and sodium
ComponentsTransporter, sodium/bile acid symporter family
KeywordsTRANSPORT PROTEIN / Bile acid transporter / ASBT / NTCP / SLC10
Function / homologybile acid:sodium symporter activity / Bile 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 / GLYCINE / Transporter, sodium/bile acid symporter family
Function and homology information
Biological speciesYersinia frederiksenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.247 Å
AuthorsWang, X. / Lyu, Y. / Ji, Y. / Sun, Z. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31770783 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

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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)34,2806
Polymers33,3881
Non-polymers8925
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.469, 185.578, 75.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 52 molecules

#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical ChemComp-A6L / 2,3-dihydroxypropyl (9Z)-octadec-9-enoate / monoolein


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 8.5
Details: 0.05 M Na2SO4, 0.05 M Li2SO4, 0.05 M Tris-HCl pH 8.5, 35% PEG 400, 0.8 mM CHAPSO, with 100 mM glycine pH 7.3 soaking

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.247→38.066 Å / Num. obs: 15449 / % possible obs: 98.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 36.58 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.057 / Rrim(I) all: 0.128 / Net I/σ(I): 10.4 / Num. measured all: 78877
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
2.247-2.2855.30.91941027760.4490.4481.0291.999.1
6.09-38.06650.03340228090.9990.0160.03731.593.2

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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: 2.247→34.8 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 733 4.75 %
Rwork0.2073 14695 -
obs0.209 15428 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.99 Å2 / Biso mean: 45.0129 Å2 / Biso min: 28.22 Å2
Refinement stepCycle: final / Resolution: 2.247→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 60 47 2443
Biso mean--69.96 50.1 -
Num. residues----311
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.247-2.420.3021600.2187288699
2.42-2.66350.25041290.2158294299
2.6635-3.04870.24471590.2057289599
3.0487-3.84020.24021520.2012296499
3.8402-34.80.22791330.2072300896
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)
11.7348-0.0409-0.33367.7316-1.9942.0852-0.1842-0.26070.46481.0840.48610.2149-0.3293-0.5108-0.20510.5175-0.03490.05840.5241-0.08950.434-13.3109-19.95613.5707
21.8411-0.42130.60812.2005-0.66511.77330.0662-0.2273-0.2456-0.0094-0.06050.45790.2892-0.3737-0.03840.2745-0.03640.02690.3685-0.03350.4044-17.5892-30.84471.0781
31.81160.6979-0.1721.3470.05211.1184-0.0876-0.0221-0.0995-0.01770.1145-0.0528-0.014-0.0302-0.0420.37450.02730.02070.3579-0.01950.33320.5279-23.2924-5.0174
43.6165-2.1877-0.25992.85980.27170.97150.22950.35210.4085-0.3798-0.2273-0.02870.0635-0.1772-0.02890.4840.0196-0.01410.43290.01820.3985-10.4748-29.9207-12.8164
51.2442-2.1821.77384.3526-2.89362.96910.1647-0.15860.2605-0.3817-0.3133-0.05470.49740.0790.10360.347-0.04160.03430.4203-0.03380.4712-18.3413-21.04661.8542
61.01090.24990.39791.3006-0.00870.76720.00370.0277-0.05330.11830.056-0.13960.0269-0.0448-0.01160.36720.0270.01140.3805-0.00130.33191.9673-26.27092.9419
71.09350.26430.71273.62770.31471.70680.0303-0.14430.1446-0.1043-0.1643-0.1222-0.2773-0.15560.15750.42610.00840.03490.37750.00720.3806-0.5313-18.82668.8728
8222222-1.32992.0422-0.48392.68946.9753-10.5641-4.190913.4792-5.66320.4654-0.0449-0.14790.9847-0.41480.6325-8.853-26.7041.7969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 22 )A-4 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 48 )A23 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 144 )A49 - 144
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 178 )A145 - 178
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 208 )A179 - 208
6X-RAY DIFFRACTION6chain 'A' and (resid 209 through 273 )A209 - 273
7X-RAY DIFFRACTION7chain 'A' and (resid 274 through 306 )A274 - 306
8X-RAY DIFFRACTION8chain 'A' and (resid 401 through 401 )A401

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