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- PDB-2xq9: Pentameric ligand gated ion channel GLIC mutant E221A in complex ... -

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Basic information

Entry
Database: PDB / ID: 2xq9
TitlePentameric ligand gated ion channel GLIC mutant E221A in complex with tetraethylarsonium (TEAs)
ComponentsGLR4197 PROTEIN
KeywordsMEMBRANE PROTEIN / OPEN CHANNEL BLOCK
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / 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 / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / 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 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / 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
ARSENIC / Proton-gated ion channel
Similarity search - Component
Biological speciesGLOEOBACTER VIOLACEUS PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.2 Å
AuthorsHilf, R.J.C. / Bertozzi, C. / Zimmermann, I. / Reiter, A. / Trauner, D. / Dutzler, R.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural Basis of Open Channel Block in a Prokaryotic Pentameric Ligand-Gated Ion Channel
Authors: Hilf, R.J.C. / Bertozzi, C. / Zimmermann, I. / Reiter, A. / Trauner, D. / Dutzler, R.
#1: Journal: Nature / Year: 2009
Title: Structure of a Potentially Open State of a Proton-Activated Pentameric Ligand-Gated Ion Channel.
Authors: Hilf, R.J.C. / Dutzler, R.
History
DepositionSep 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: GLR4197 PROTEIN
B: GLR4197 PROTEIN
C: GLR4197 PROTEIN
D: GLR4197 PROTEIN
E: GLR4197 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,3936
Polymers181,3185
Non-polymers751
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20550 Å2
ΔGint-154.3 kcal/mol
Surface area63410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.314, 128.310, 164.374
Angle α, β, γ (deg.)90.00, 104.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 7:316 )
211CHAIN B AND (RESSEQ 7:316 )
311CHAIN C AND (RESSEQ 7:316 )
411CHAIN D AND (RESSEQ 7:316 )
511CHAIN E AND (RESSEQ 7:316 )

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Components

#1: Protein
GLR4197 PROTEIN / GLIC


Mass: 36263.695 Da / Num. of mol.: 5 / Fragment: RESIDUES 43-359 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GLOEOBACTER VIOLACEUS PCC 7421 (bacteria)
Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7NDN8
#2: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: As
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 264 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 264 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, GLU 264 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 264 TO ASP ENGINEERED RESIDUE IN CHAIN C, GLU 264 TO ASP ENGINEERED RESIDUE IN CHAIN D, GLU 264 TO ASP ENGINEERED RESIDUE IN CHAIN E, GLU 264 TO ASP

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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: 5.32 Å3/Da / Density % sol: 76.68 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 9% PEG 4000, 50MM CH3COONA, 200MM (NH4)2SO4, PH 4.0, VAPOR DIFFUSION, TEMPERATURE 277.15K, VAPOR DIFFUSION, HANGING DROP.

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.045
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 68086 / % possible obs: 91.1 % / Observed criterion σ(I): 3.2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.2→40 Å / SU ML: 0.4 / σ(F): 1.9 / Phase error: 33.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 2802 4.6 %
Rwork0.2516 --
obs0.2519 60862 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.551 Å2 / ksol: 0.268 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-23.56 Å2-0 Å2-46.1976 Å2
2---19.8901 Å2-0 Å2
3----7.7213 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12600 0 1 0 12601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112940
X-RAY DIFFRACTIONf_angle_d1.31817680
X-RAY DIFFRACTIONf_dihedral_angle_d16.0334620
X-RAY DIFFRACTIONf_chiral_restr0.0822060
X-RAY DIFFRACTIONf_plane_restr0.0052215
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2520X-RAY DIFFRACTIONPOSITIONAL
12B2520X-RAY DIFFRACTIONPOSITIONAL0.061
13C2520X-RAY DIFFRACTIONPOSITIONAL0.048
14D2520X-RAY DIFFRACTIONPOSITIONAL0.056
15E2520X-RAY DIFFRACTIONPOSITIONAL0.06
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.25520.3631260.36532937X-RAY DIFFRACTION100
3.2552-3.31430.3377660.34352997X-RAY DIFFRACTION100
3.3143-3.37810.31391120.3152939X-RAY DIFFRACTION100
3.3781-3.4470.33171410.30552862X-RAY DIFFRACTION100
3.447-3.52190.29791600.29012869X-RAY DIFFRACTION100
3.5219-3.60380.35361450.2912891X-RAY DIFFRACTION100
3.6038-3.69380.33391280.27812865X-RAY DIFFRACTION100
3.6938-3.79360.30711700.2642881X-RAY DIFFRACTION100
3.7936-3.90520.28491510.25712907X-RAY DIFFRACTION100
3.9052-4.03110.26881580.24652873X-RAY DIFFRACTION100
4.0311-4.1750.27681670.24462901X-RAY DIFFRACTION100
4.175-4.3420.27641360.23242875X-RAY DIFFRACTION100
4.342-4.53940.23481490.20632898X-RAY DIFFRACTION100
4.5394-4.77830.17841600.18152890X-RAY DIFFRACTION100
4.7783-5.07710.21961610.18722885X-RAY DIFFRACTION100
5.0771-5.46830.2131670.20212871X-RAY DIFFRACTION100
5.4683-6.01690.32871450.24092911X-RAY DIFFRACTION100
6.0169-6.88380.2732880.26132998X-RAY DIFFRACTION100
6.8838-8.65860.2941860.24022888X-RAY DIFFRACTION100
8.6586-40.20290.18131860.28422922X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.9385 Å / Origin y: 3.3601 Å / Origin z: 52.6167 Å
111213212223313233
T0.0314 Å2-0.0797 Å20.0599 Å2-0.045 Å20.0307 Å2---0.048 Å2
L0.8213 °20.0462 °20.4157 °2-0.8875 °20.202 °2--1.0764 °2
S-0.0017 Å °-0.0039 Å °0.0592 Å °0.2021 Å °-0.0986 Å °-0.0679 Å °-0.0016 Å °-0.027 Å °0.0461 Å °
Refinement TLS groupSelection details: ALL

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