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- PDB-2xqa: Pentameric ligand gated ion channel GLIC in complex with tetrabut... -

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Basic information

Entry
Database: PDB / ID: 2xqa
TitlePentameric ligand gated ion channel GLIC in complex with tetrabutylantimony (TBSb)
ComponentsGLR4197 PROTEIN
KeywordsMEMBRANE PROTEIN / OPEN CHANNEL BLOCK
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane transporter complex / 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 / 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
ANTIMONY (III) ION / Proton-gated ion channel
Similarity search - Component
Biological speciesGLOEOBACTER VIOLACEUS PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.7 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)181,5106
Polymers181,3895
Non-polymers1221
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20610 Å2
ΔGint-138.5 kcal/mol
Surface area64610 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
Details: SB ION
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-SB / ANTIMONY (III) ION


Mass: 121.760 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sb
Sequence detailsRESIDUES 50-359

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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: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 9% PEG4000, 50MM CH3COONA, 200MM (NH4)2SO4, PH4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.15K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 277.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.8
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 3.6→40.2 Å / Num. obs: 43105 / % possible obs: 99.4 % / Observed criterion σ(I): 2.2 / Redundancy: 5.6 % / Biso Wilson estimate: 92.5 Å2 / Rmerge(I) obs: 0.09

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Processing

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

Resolution: 3.7→40.2 Å / SU ML: 0.59 / σ(F): 1.9 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 1906 5 %
Rwork0.2558 --
obs0.2567 37865 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.467 Å2 / ksol: 0.276 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-28.4391 Å20 Å2-48.6598 Å2
2---28.0161 Å20 Å2
3----0.423 Å2
Refinement stepCycle: LAST / Resolution: 3.7→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_d1.38217685
X-RAY DIFFRACTIONf_dihedral_angle_d17.7434625
X-RAY DIFFRACTIONf_chiral_restr0.0892060
X-RAY DIFFRACTIONf_plane_restr0.0062215
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2521X-RAY DIFFRACTIONPOSITIONAL
12B2521X-RAY DIFFRACTIONPOSITIONAL0.059
13C2521X-RAY DIFFRACTIONPOSITIONAL0.049
14D2521X-RAY DIFFRACTIONPOSITIONAL0.054
15E2521X-RAY DIFFRACTIONPOSITIONAL0.058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.79250.43251220.36432368X-RAY DIFFRACTION89
3.7925-3.8950.37021400.34062586X-RAY DIFFRACTION97
3.895-4.00950.35881450.30262627X-RAY DIFFRACTION98
4.0095-4.13880.31791430.28012583X-RAY DIFFRACTION98
4.1388-4.28650.27591290.26112628X-RAY DIFFRACTION98
4.2865-4.45790.27711270.25482595X-RAY DIFFRACTION97
4.4579-4.66060.24671610.22082543X-RAY DIFFRACTION96
4.6606-4.90590.25641220.21242585X-RAY DIFFRACTION96
4.9059-5.21260.26331220.20082601X-RAY DIFFRACTION97
5.2126-5.61410.23121620.2222581X-RAY DIFFRACTION96
5.6141-6.17730.30351590.24072552X-RAY DIFFRACTION96
6.1773-7.06690.3083750.24192650X-RAY DIFFRACTION96
7.0669-8.88770.32751250.22072563X-RAY DIFFRACTION94
8.8877-40.20210.17441740.26892497X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 24.9164 Å / Origin y: 3.1883 Å / Origin z: 52.6059 Å
111213212223313233
T0.0352 Å2-0.0203 Å20.0788 Å2-0.1099 Å20.0061 Å2---0.0323 Å2
L0.242 °2-0.032 °20.2184 °2-0.26 °20.099 °2--0.3125 °2
S0.017 Å °0.0266 Å °0.027 Å °0.0628 Å °-0.0363 Å °-0.0334 Å °0.0102 Å °-0.0448 Å °-0.0148 Å °
Refinement TLS groupSelection details: ALL

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