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- PDB-5lid: X-ray structure of a pentameric ligand gated ion channel from Erw... -

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Basic information

Entry
Database: PDB / ID: 5lid
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromopromazine
ComponentsCys-loop ligand-gated ion channel
KeywordsTRANSPORT PROTEIN / ligand-gated ion channel
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
bromopromazine / Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsNys, M. / Wijckmans, E. / Farinha, A. / Brams, M. / Spurny, R. / Ulens, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine.
Authors: Nys, M. / Wijckmans, E. / Farinha, A. / Yoluk, O. / Andersson, M. / Brams, M. / Spurny, R. / Peigneur, S. / Tytgat, J. / Lindahl, E. / Ulens, C.
History
DepositionJul 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cys-loop ligand-gated ion channel
B: Cys-loop ligand-gated ion channel
C: Cys-loop ligand-gated ion channel
D: Cys-loop ligand-gated ion channel
E: Cys-loop ligand-gated ion channel
F: Cys-loop ligand-gated ion channel
G: Cys-loop ligand-gated ion channel
H: Cys-loop ligand-gated ion channel
I: Cys-loop ligand-gated ion channel
J: Cys-loop ligand-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,10030
Polymers353,83410
Non-polymers7,26620
Water00
1
A: Cys-loop ligand-gated ion channel
B: Cys-loop ligand-gated ion channel
C: Cys-loop ligand-gated ion channel
D: Cys-loop ligand-gated ion channel
E: Cys-loop ligand-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,55015
Polymers176,9175
Non-polymers3,63310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24850 Å2
ΔGint-158 kcal/mol
Surface area67300 Å2
MethodPISA
2
F: Cys-loop ligand-gated ion channel
G: Cys-loop ligand-gated ion channel
H: Cys-loop ligand-gated ion channel
I: Cys-loop ligand-gated ion channel
J: Cys-loop ligand-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,55015
Polymers176,9175
Non-polymers3,63310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25190 Å2
ΔGint-165 kcal/mol
Surface area66940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.720, 267.910, 111.330
Angle α, β, γ (deg.)90.00, 106.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cys-loop ligand-gated ion channel / ELIC


Mass: 35383.367 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#2: Chemical
ChemComp-6XY / bromopromazine


Mass: 363.315 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C17H19BrN2S

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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: 4.27 Å3/Da / Density % sol: 71.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium sulfate, 50 mM ADA pH 6.5, 9-12 % PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.91983 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91983 Å / Relative weight: 1
ReflectionResolution: 3.7→49.54 Å / Num. obs: 69231 / % possible obs: 99.8 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.5→49.537 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 3426 4.95 %
Rwork0.2125 --
obs0.2148 69231 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.5→49.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25050 0 20 0 25070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00525730
X-RAY DIFFRACTIONf_angle_d1.21935070
X-RAY DIFFRACTIONf_dihedral_angle_d15.6429230
X-RAY DIFFRACTIONf_chiral_restr0.0453900
X-RAY DIFFRACTIONf_plane_restr0.0054470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5-4.56420.24661430.23952736X-RAY DIFFRACTION100
4.5642-4.63230.2851440.22062814X-RAY DIFFRACTION100
4.6323-4.70470.2621400.2172668X-RAY DIFFRACTION100
4.7047-4.78170.25531470.20522783X-RAY DIFFRACTION100
4.7817-4.86410.25371420.2032750X-RAY DIFFRACTION100
4.8641-4.95250.22451410.19752713X-RAY DIFFRACTION100
4.9525-5.04760.23761480.20192780X-RAY DIFFRACTION100
5.0476-5.15060.23461420.1882732X-RAY DIFFRACTION100
5.1506-5.26240.21891460.18812761X-RAY DIFFRACTION100
5.2624-5.38470.25751410.19032700X-RAY DIFFRACTION100
5.3847-5.51920.22911440.19192780X-RAY DIFFRACTION100
5.5192-5.66820.23511410.20562723X-RAY DIFFRACTION100
5.6682-5.83480.25691470.2022788X-RAY DIFFRACTION100
5.8348-6.02280.28691410.20582681X-RAY DIFFRACTION100
6.0228-6.23770.25051420.21622789X-RAY DIFFRACTION100
6.2377-6.48690.31741430.22652769X-RAY DIFFRACTION100
6.4869-6.78140.34091430.24362711X-RAY DIFFRACTION100
6.7814-7.1380.27961400.22562729X-RAY DIFFRACTION100
7.138-7.58370.28681480.21292795X-RAY DIFFRACTION100
7.5837-8.16690.23241400.19722708X-RAY DIFFRACTION100
8.1669-8.98430.25131420.1712742X-RAY DIFFRACTION100
8.9843-10.27430.16881430.15122748X-RAY DIFFRACTION100
10.2743-12.90650.22041380.1862696X-RAY DIFFRACTION98
12.9065-49.54040.33351400.30772709X-RAY DIFFRACTION98
Refinement TLS params.Method: refined
Refinement TLS groupSelection details: chain 'd' and resid ' 1 ' and name 'BR ' and altloc ' '

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