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- PDB-5l4e: X-ray structure of the 2-22' locally-closed mutant of GLIC in com... -

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Basic information

Entry
Database: PDB / ID: 5l4e
TitleX-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / membrane protein / barbiturates / transport protein
Function / homologyNeurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel / sodium channel activity / potassium channel activity / nervous system process / extracellular ligand-gated ion channel activity ...Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel / sodium channel activity / potassium channel activity / nervous system process / extracellular ligand-gated ion channel activity / ion transmembrane transport / regulation of membrane potential / transmembrane signaling receptor activity / chemical synaptic transmission / synapse / neuron projection / integral component of plasma membrane / signal transduction / identical protein binding / Proton-gated ion channel
Function and homology information
Specimen sourceGloeobacter (Cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsFourati, Z. / Ruza, R.R. / Delarue, M.
Funding supportFrance , 1 items
OrganizationGrant numberCountry
French National Research Agency13BSV8002002France
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 25, 2016 / Release: Dec 21, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 21, 2016Structure modelrepositoryInitial release
1.1Dec 28, 2016Structure modelDatabase references
1.2Feb 15, 2017Structure modelDatabase references
1.3Sep 6, 2017Structure modelAdvisory / Author supporting evidencepdbx_audit_support / pdbx_unobs_or_zero_occ_atoms_pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)181,71812
Polyers181,1285
Non-polymers5907
Water37821
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)23590
ΔGint (kcal/M)-192
Surface area (Å2)63330
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)182.025, 134.581, 159.018
Angle α, β, γ (deg.)90.00, 101.88, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

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


Mass: 36225.605 Da / Num. of mol.: 5 / Source: (gene. exp.) Gloeobacter (Cyanobacteria) / Gene: glvI, glr4197 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#2: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Formula: C12H26 / Dodecane
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Formula: Cl / Chloride
#4: Chemical ChemComp-EDP / 5-ethyl-5-[(2R)-pentan-2-yl]-2-thioxodihydropyrimidine-4,6(1H,5H)-dione / Thiopental


Mass: 242.338 Da / Num. of mol.: 1 / Formula: C11H18N2O2S / Sodium thiopental
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Formula: H2O / Water

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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: 5.26 Å3/Da / Density % sol: 76.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100 mM NaAcetate pH4 200 NaSCN 12-15% PEG4000 16% glycerol 3%DMSO
pH range: 4-5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→49 Å / Num. obs: 47093 / % possible obs: 99.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 83.88 Å2 / Net I/σ(I): 9.4
Reflection shellResolution: 3.5→3.69 Å / Mean I/σ(I) obs: 1.9 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 3.5→40.41 Å / Cor.coef. Fo:Fc: 0.7938 / Cor.coef. Fo:Fc free: 0.794 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.432
RfactorNum. reflection% reflectionSelection details
Rfree0.249323805.06 %RANDOM
Rwork0.2286---
obs0.22974707799.22 %-
Displacement parametersBiso mean: 127.18 Å2
Baniso -1Baniso -2Baniso -3
1--22.9248 Å20 Å267.4466 Å2
2---2.8926 Å20 Å2
3---25.8173 Å2
Refine analyzeLuzzati coordinate error obs: 0.561 Å
Refinement stepCycle: 1 / Resolution: 3.5→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms126000332112654
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumberRestraint functionWeight
t_bond_d0.0112972HARMONIC2
t_angle_deg1.1117738HARMONIC2
t_dihedral_angle_d4294SINUSOIDAL2
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes260HARMONIC2
t_gen_planes1877HARMONIC5
t_it12972HARMONIC20
t_nbd
t_omega_torsion2.78
t_other_torsion18.34
t_improper_torsion
t_chiral_improper_torsion1761SEMIHARMONIC5
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact15234SEMIHARMONIC4
Refine LS shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3241795.23 %
Rwork0.29673246-
all0.29813425-
obs--98 %

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