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- PDB-5l4h: X-ray structure of the 2-22' locally-closed mutant of GLIC in com... -

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Basic information

Entry
Database: PDB / ID: 5l4h
TitleX-ray structure of the 2-22' locally-closed mutant of GLIC in complex with 5-(2-BROMO-ETHYL)-5-ETHYL-PYRIMIDINE-2,4,6-TRIONE (brominated barbiturate)
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / transmembrane transporter complex / 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
Chem-6JW / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsFourati, Z. / Ruza, R.R. / Delarue, M.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State.
Authors: Fourati, Z. / Ruza, R.R. / Laverty, D. / Drege, E. / Delarue-Cochin, S. / Joseph, D. / Koehl, P. / Smart, T. / Delarue, M.
History
DepositionMay 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
D: Proton-gated ion channel
E: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,07912
Polymers181,1285
Non-polymers9517
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23180 Å2
ΔGint-199 kcal/mol
Surface area64750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.145, 127.942, 159.700
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC


Mass: 36225.605 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria)
Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-6JW / 5-(2-bromoethyl)-5-ethyl-1,3-diazinane-2,4,6-trione


Mass: 263.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11BrN2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.9 Å3/Da / Density % sol: 74.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM NaAcetate pH4, 200 mM NaSCN, 12-15% PEG4000, 16% glycerol, 3% DMSO

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3.3→49 Å / Num. obs: 52350 / % possible obs: 99.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 85.16 Å2 / Net I/σ(I): 9.4
Reflection shellResolution: 3.3→3.48 Å / Mean I/σ(I) obs: 1.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 3.3→48 Å / Cor.coef. Fo:Fc: 0.7903 / Cor.coef. Fo:Fc free: 0.7841 / SU R Cruickshank DPI: 2.109 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.214 / SU Rfree Blow DPI: 0.366 / SU Rfree Cruickshank DPI: 0.383
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 2662 5.09 %RANDOM
Rwork0.2136 ---
obs0.2147 52350 99.29 %-
Displacement parametersBiso mean: 83.42 Å2
Baniso -1Baniso -2Baniso -3
1--20.0211 Å20 Å246.1187 Å2
2--1.8177 Å20 Å2
3---18.2034 Å2
Refine analyzeLuzzati coordinate error obs: 0.462 Å
Refinement stepCycle: 1 / Resolution: 3.3→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12597 0 31 103 12731
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112967HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.117731HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4291SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes259HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1877HARMONIC5
X-RAY DIFFRACTIONt_it12967HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion18.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1760SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15196SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2984 197 5.16 %
Rwork0.2596 3622 -
all0.2615 3819 -
obs--99.23 %

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