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- PDB-7cyk: Crystal structure of a second cysteine-pair mutant (V110C-I197C) ... -

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Basic information

Entry
Database: PDB / ID: 7cyk
TitleCrystal structure of a second cysteine-pair mutant (V110C-I197C) of a bacterial bile acid transporter before disulfide bond formation
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 / : / Ketopantoate/pantoate/pantothenate transporter PanS
Function and homology information
Biological speciesYersinia frederiksenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.785 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: An engineered disulfide bridge traps and validates an outward-facing conformation in a bile acid transporter.
Authors: Wang, X. / Lyu, Y. / Ji, Y. / Sun, Z. / Zhou, X.
History
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Transporter, sodium/bile acid symporter family
B: Transporter, sodium/bile acid symporter family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6388
Polymers65,4342
Non-polymers1,2046
Water73941
1
A: Transporter, sodium/bile acid symporter family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3194
Polymers32,7171
Non-polymers6023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-25 kcal/mol
Surface area13670 Å2
MethodPISA
2
B: Transporter, sodium/bile acid symporter family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3194
Polymers32,7171
Non-polymers6023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-24 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.421, 46.652, 70.781
Angle α, β, γ (deg.)90.000, 101.010, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 256 or resid 258 through 302 or resid 403))
21(chain B and (resid 7 through 256 or resid 258 through 302 or resid 403))

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 7 through 256 or resid 258 through 302 or resid 403))AA7 - 2567 - 256
12GLNGLNVALVAL(chain A and (resid 7 through 256 or resid 258 through 302 or resid 403))AA258 - 302258 - 302
13HGHGHGHG(chain A and (resid 7 through 256 or resid 258 through 302 or resid 403))AE403
21ARGARGGLYGLY(chain B and (resid 7 through 256 or resid 258 through 302 or resid 403))BB7 - 2567 - 256
22GLNGLNVALVAL(chain B and (resid 7 through 256 or resid 258 through 302 or resid 403))BB258 - 302258 - 302
23HGHGHGHG(chain B and (resid 7 through 256 or resid 258 through 302 or resid 403))BH403

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Components

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


Mass: 32717.088 Da / Num. of mol.: 2 / Mutation: V110C, I197C
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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 4.5
Details: 0.1 M NaCl, 0.1M Na+-citrate pH 4.5, 32% PEG 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.785→45.264 Å / Num. obs: 15615 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 53.39 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.059 / Rrim(I) all: 0.133 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.785-2.8334.810.6597800.70790.3340.741100
7.55-45.2644.510.0528310.99670.0260.05899.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7W

4n7w


Resolution: 2.785→45.264 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 772 4.95 %
Rwork0.226 14830 -
obs0.228 15602 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.26 Å2 / Biso mean: 48.2043 Å2 / Biso min: 24.29 Å2
Refinement stepCycle: final / Resolution: 2.785→45.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 10 41 4507
Biso mean--106.44 40.22 -
Num. residues----597
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2680X-RAY DIFFRACTION3.488TORSIONAL
12B2680X-RAY DIFFRACTION3.488TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7854-2.95990.32431210.25292451100
2.9599-3.18840.30631270.24692432100
3.1884-3.50920.29141150.23992476100
3.5092-4.01670.2881420.22512443100
4.0167-5.05950.24711290.21942482100
5.0595-45.2640.23431380.2126254699

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