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- PDB-2yks: PENTAMERIC LIGAND GATED ION CHANNEL ELIC MUTANT F246A -

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Basic information

Entry
Database: PDB / ID: 2yks
TitlePENTAMERIC LIGAND GATED ION CHANNEL ELIC MUTANT F246A
ComponentsCYS-LOOP LIGAND-GATED ION CHANNEL
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / PROKARYOTIC CYS-LOOP RECEPTOR / CATION SELECTIVE CHANNEL
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZimmermann, I. / Dutzler, R.
CitationJournal: Plos Biol. / Year: 2011
Title: Ligand Activation of the Prokaryotic Pentameric Ligand-Gated Ion Channel Elic.
Authors: Zimmermann, I. / Dutzler, R.
History
DepositionMay 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)367,45910
Polymers367,45910
Non-polymers00
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


Theoretical massNumber of molelcules
Total (without water)183,7295
Polymers183,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24350 Å2
ΔGint-134 kcal/mol
Surface area68160 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


Theoretical massNumber of molelcules
Total (without water)183,7295
Polymers183,7295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24230 Å2
ΔGint-133.5 kcal/mol
Surface area68260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.502, 266.147, 110.851
Angle α, β, γ (deg.)90.00, 109.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 11:316 )
211CHAIN B AND (RESSEQ 11:316 )
311CHAIN C AND (RESSEQ 11:316 )
411CHAIN D AND (RESSEQ 11:316 )
511CHAIN E AND (RESSEQ 11:316 )
611CHAIN F AND (RESSEQ 11:316 )
711CHAIN G AND (RESSEQ 11:316 )
811CHAIN H AND (RESSEQ 11:316 )
911CHAIN I AND (RESSEQ 11:316 )
1011CHAIN J AND (RESSEQ 11:316 )

NCS oper:
IDCodeMatrixVector
1given(0.3129, 0.9111, -0.2682), (-0.9378, 0.3411, 0.0648), (0.1505, 0.2312, 0.9612)-42.7832, -124.505, 23.8259
2given(-0.7953, 0.536, -0.2832), (-0.6056, -0.7234, 0.3316), (-0.0271, 0.4352, 0.8999)-175.6276, -125.9225, 11.4395
3given(-0.7987, -0.6012, -0.0254), (0.5322, -0.7254, 0.4365), (-0.2809, 0.3351, 0.8993)-215.7059, -2.6809, -19.4771
4given(0.3117, -0.9387, 0.1474), (0.9117, 0.3392, 0.232), (-0.2678, 0.062, 0.9615)-107.4661, 75.8891, -27.0288
5given(-0.0368, 0.0834, -0.9958), (-0.001, 0.9965, 0.0835), (0.9993, 0.004, -0.0366)-132.9228, 69.4292, 34.9397
6given(-0.2811, 0.9298, -0.2376), (0.0951, 0.2733, 0.9572), (0.955, 0.2464, -0.1653)-31.4492, 27.3766, 54.3869
7given(-0.2601, 0.4779, 0.839), (0.3541, -0.7612, 0.5433), (0.8983, 0.4385, 0.0287)-41.9641, -82.0216, 78.4957
8given(0.0019, -0.6568, 0.7541), (0.4224, -0.683, -0.5959), (0.9064, 0.3197, 0.2761)-151.0505, -108.405, 74.3211
9given(0.1401, -0.9155, -0.3772), (0.1977, 0.3991, -0.8953), (0.9702, 0.0508, 0.237)-209.1301, -15.6469, 47.4947

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Components

#1: Protein
CYS-LOOP LIGAND-GATED ION CHANNEL / ELIC


Mass: 36745.855 Da / Num. of mol.: 10 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA CHRYSANTHEMI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C7B7
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 246 TO ALA ENGINEERED RESIDUE IN CHAIN B, PHE 246 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, PHE 246 TO ALA ENGINEERED RESIDUE IN CHAIN B, PHE 246 TO ALA ENGINEERED RESIDUE IN CHAIN C, PHE 246 TO ALA ENGINEERED RESIDUE IN CHAIN D, PHE 246 TO ALA ENGINEERED RESIDUE IN CHAIN E, PHE 246 TO ALA ENGINEERED RESIDUE IN CHAIN F, PHE 246 TO ALA ENGINEERED RESIDUE IN CHAIN G, PHE 246 TO ALA ENGINEERED RESIDUE IN CHAIN H, PHE 246 TO ALA ENGINEERED RESIDUE IN CHAIN I, PHE 246 TO ALA ENGINEERED RESIDUE IN CHAIN J, PHE 246 TO ALA

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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: 3.99 Å3/Da / Density % sol: 69.19 % / Description: NONE
Crystal growpH: 6.5 / Details: 50MM ADA PH6.5, 200MM NALISO4, 10% (W/V) PEG4000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.045
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 3.3→133.07 Å / Num. obs: 140127 / % possible obs: 88.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 103.02 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.08
Reflection shellResolution: 3.38→10.09 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.9 / % possible all: 78.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL0

2vl0


Resolution: 3.3→19.97 Å / SU ML: 0.43 / σ(F): 0 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 4267 5.1 %
Rwork0.242 --
obs0.243 84276 98.2 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.18 Å2 / ksol: 0.27 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7051 Å20 Å229.1687 Å2
2---23.5347 Å20 Å2
3---15.8296 Å2
Refinement stepCycle: LAST / Resolution: 3.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24950 0 0 0 24950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01525620
X-RAY DIFFRACTIONf_angle_d1.51634930
X-RAY DIFFRACTIONf_dihedral_angle_d16.7389200
X-RAY DIFFRACTIONf_chiral_restr0.1023900
X-RAY DIFFRACTIONf_plane_restr0.0114450
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2495X-RAY DIFFRACTIONPOSITIONAL
12B2495X-RAY DIFFRACTIONPOSITIONAL0.129
13C2495X-RAY DIFFRACTIONPOSITIONAL0.122
14D2495X-RAY DIFFRACTIONPOSITIONAL0.14
15E2495X-RAY DIFFRACTIONPOSITIONAL0.122
16F2495X-RAY DIFFRACTIONPOSITIONAL0.128
17G2495X-RAY DIFFRACTIONPOSITIONAL0.138
18H2495X-RAY DIFFRACTIONPOSITIONAL0.109
19I2495X-RAY DIFFRACTIONPOSITIONAL0.127
110J2495X-RAY DIFFRACTIONPOSITIONAL0.124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.33750.4171830.41421575X-RAY DIFFRACTION59
3.3375-3.37650.47291290.39032543X-RAY DIFFRACTION93
3.3765-3.41750.39611520.36442694X-RAY DIFFRACTION100
3.4175-3.46060.35571380.35042706X-RAY DIFFRACTION100
3.4606-3.50590.38071450.34562685X-RAY DIFFRACTION100
3.5059-3.55360.35151430.34022713X-RAY DIFFRACTION100
3.5536-3.60410.41061530.32442677X-RAY DIFFRACTION100
3.6041-3.65760.32981490.31222724X-RAY DIFFRACTION100
3.6576-3.71440.3181310.30412714X-RAY DIFFRACTION100
3.7144-3.77490.32741610.31042718X-RAY DIFFRACTION100
3.7749-3.83950.32671360.27812700X-RAY DIFFRACTION100
3.8395-3.90880.31081470.27472721X-RAY DIFFRACTION100
3.9088-3.98340.28521490.27052681X-RAY DIFFRACTION100
3.9834-4.06410.28911370.26992724X-RAY DIFFRACTION100
4.0641-4.15170.32061300.24722708X-RAY DIFFRACTION100
4.1517-4.24730.28741400.24552725X-RAY DIFFRACTION100
4.2473-4.35250.28531450.23342686X-RAY DIFFRACTION100
4.3525-4.46890.27021440.222724X-RAY DIFFRACTION100
4.4689-4.59890.20811650.2032707X-RAY DIFFRACTION100
4.5989-4.74540.20311290.19532708X-RAY DIFFRACTION100
4.7454-4.91260.25291350.20552719X-RAY DIFFRACTION100
4.9126-5.10610.22231440.2052693X-RAY DIFFRACTION100
5.1061-5.33430.22151620.20472730X-RAY DIFFRACTION100
5.3343-5.60960.23581470.20992712X-RAY DIFFRACTION100
5.6096-5.95230.20821530.2082702X-RAY DIFFRACTION100
5.9523-6.39780.21511470.22192716X-RAY DIFFRACTION100
6.3978-7.01620.29491330.25142754X-RAY DIFFRACTION100
7.0162-7.97430.27261580.2332684X-RAY DIFFRACTION99
7.9743-9.84240.19241350.19262742X-RAY DIFFRACTION100
9.8424-19.97010.24591470.23412724X-RAY DIFFRACTION99

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