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

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Basic information

Entry
Database: PDB / ID: 6lgv
TitleCrystal structure of a cysteine-pair mutant (P10C-S291C) of a bacterial bile acid transporter in an inward-facing state complexed with citrate
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 / CITRIC ACID / Ketopantoate/pantoate/pantothenate transporter PanS
Function and homology information
Biological speciesYersinia frederiksenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.847 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 1.3Oct 30, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,3637
Polymers33,3881
Non-polymers1,9756
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint1 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.798, 91.779, 44.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-A6L / 2,3-dihydroxypropyl (9Z)-octadec-9-enoate / monoolein


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 4.5
Details: 0.1 M NaCl, 0.1 M MgCl2, 0.1 M Na+-citrate pH 4.5, 32% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.847→40.3 Å / Num. obs: 24982 / % possible obs: 95.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 25.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.044 / Rrim(I) all: 0.112 / Net I/σ(I): 12.1 / Num. measured all: 156974
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
1.847-1.8796.71.032866813020.8130.431.121.9100
5.012-40.36.10.038866214250.9990.0170.04233.399.3

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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: 4N7W

4n7w


Resolution: 1.847→40.3 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1327 5.32 %
Rwork0.1984 23635 -
obs0.2003 24962 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.56 Å2 / Biso mean: 27.129 Å2 / Biso min: 10.56 Å2
Refinement stepCycle: final / Resolution: 1.847→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 138 123 2595
Biso mean--43.4 33.2 -
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 (%)
1.8474-1.92140.25941840.2168265299
1.9214-2.00880.25021370.21872714100
2.0088-2.11470.2591470.21232709100
2.1147-2.24720.24941340.20842730100
2.2472-2.42070.22421620.19342678100
2.4207-2.66430.23171430.1926227999
2.6643-3.04970.24931350.1878235999
3.0497-3.84180.241380.1843264295
3.8418-40.30.21851470.2049287298

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