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- PDB-2xq3: Pentameric ligand gated ion channel GLIC in complex with Br-lidocaine -

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Basic information

Entry
Database: PDB / ID: 2xq3
TitlePentameric ligand gated ion channel GLIC in complex with Br-lidocaine
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
BROMIDE ION / Proton-gated ion channel
Similarity search - Component
Biological speciesGLOEOBACTER VIOLACEUS PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.5 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)181,4696
Polymers181,3895
Non-polymers801
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21550 Å2
ΔGint-145.5 kcal/mol
Surface area64620 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 / PENTAMERIC LIGAND GATED ION CHANNEL


Mass: 36277.723 Da / Num. of mol.: 5 / Fragment: RESIDUES 43-359
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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br

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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: 5.31 Å3/Da / Density % sol: 76.67 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 9% PEG 4000, 50 MM CH3COONA, 200 MM (NH4)2SO4, PH 4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K.

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9191
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 45222 / % possible obs: 86.8 % / Observed criterion σ(I): 2.3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6

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Processing

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

Resolution: 3.5→40.2 Å / SU ML: 0.49 / σ(F): 1.91 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2234 5 %
Rwork0.2477 --
obs0.2482 44442 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.195 Å2 / ksol: 0.257 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.7708 Å20 Å2-54.9218 Å2
2---15.5308 Å20 Å2
3----6.2401 Å2
Refinement stepCycle: LAST / Resolution: 3.5→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12605 0 1 0 12606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112945
X-RAY DIFFRACTIONf_angle_d1.40117685
X-RAY DIFFRACTIONf_dihedral_angle_d17.5464625
X-RAY DIFFRACTIONf_chiral_restr0.0912060
X-RAY DIFFRACTIONf_plane_restr0.0052215
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2521X-RAY DIFFRACTIONPOSITIONAL
12B2521X-RAY DIFFRACTIONPOSITIONAL0.056
13C2521X-RAY DIFFRACTIONPOSITIONAL0.048
14D2521X-RAY DIFFRACTIONPOSITIONAL0.054
15E2521X-RAY DIFFRACTIONPOSITIONAL0.057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.57610.3771710.35631564X-RAY DIFFRACTION57
3.5761-3.65920.3671160.33942441X-RAY DIFFRACTION88
3.6592-3.75070.36161610.3222644X-RAY DIFFRACTION97
3.7507-3.8520.3271470.30892710X-RAY DIFFRACTION98
3.852-3.96520.34181330.29192702X-RAY DIFFRACTION98
3.9652-4.09310.32741470.25392761X-RAY DIFFRACTION99
4.0931-4.23920.22831490.23912686X-RAY DIFFRACTION99
4.2392-4.40880.27081370.24112739X-RAY DIFFRACTION98
4.4088-4.60920.25111460.21192693X-RAY DIFFRACTION98
4.6092-4.85180.21321430.18992737X-RAY DIFFRACTION98
4.8518-5.15520.2061420.18922718X-RAY DIFFRACTION98
5.1552-5.55230.24841670.21272729X-RAY DIFFRACTION99
5.5523-6.10930.32341540.25432733X-RAY DIFFRACTION99
6.1093-6.98930.2751770.24542841X-RAY DIFFRACTION100
6.9893-8.79060.29141570.22222767X-RAY DIFFRACTION99
8.7906-40.20230.16871870.26142743X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 24.9034 Å / Origin y: 3.0861 Å / Origin z: 52.6074 Å
111213212223313233
T0.1831 Å2-0.0919 Å20.0894 Å2-0.2651 Å20.0408 Å2--0.2468 Å2
L0.5673 °20.043 °20.4459 °2-0.7197 °20.191 °2--1.1405 °2
S-0.0088 Å °0.0284 Å °0.0356 Å °0.1199 Å °-0.0842 Å °-0.0389 Å °-0.0634 Å °-0.0236 Å °0 Å °
Refinement TLS groupSelection details: ALL

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