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- PDB-5l47: X-ray structure of the 2-22' locally-closed mutant of GLIC in com... -

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Basic information

Entry
Database: PDB / ID: 5l47
TitleX-ray structure of the 2-22' locally-closed mutant of GLIC in complex with cyanoselenobarbital (seleniated barbiturate)
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium 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-6JA / ACETATE ION / DODECANE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsReinholds Ruza, R. / Fourati, Z. / Delarue, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency13BSV8002002 France
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 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)182,15121
Polymers181,1285
Non-polymers1,02316
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25170 Å2
ΔGint-239 kcal/mol
Surface area64780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.158, 128.124, 162.193
Angle α, β, γ (deg.)90.00, 102.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 5 molecules ABCDE

#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 (bacteria) / Strain: PCC 7421 / Tissue: Memrane / Gene: glvI, glr4197 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q7NDN8

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Non-polymers , 6 types, 123 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-6JA / 2-[5-ethyl-2,4,6-tris(oxidanylidene)-1,3-diazinan-5-yl]ethyl selenocyanate


Mass: 288.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N3O3Se
#6: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 5.07 Å3/Da / Density % sol: 75.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100 mM Na Acetate pH4, 200 mM Na SCN, 12-15% PEG4000, 3% DMSO, 16% glycerol
PH range: 4-5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 72625 / % possible obs: 99.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 93.49 Å2 / Net I/σ(I): 9.4
Reflection shellResolution: 2.99→3.15 Å / Redundancy: 3.1 % / 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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TLV.pdb
Resolution: 3.3→49 Å / Cor.coef. Fo:Fc: 0.8344 / Cor.coef. Fo:Fc free: 0.8028 / SU R Cruickshank DPI: 0.607 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.535 / SU Rfree Blow DPI: 0.3 / SU Rfree Cruickshank DPI: 0.313
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 3329 5.07 %RANDOM
Rwork0.2096 ---
obs0.2106 47093 99.3 %-
Displacement parametersBiso mean: 89.93 Å2
Baniso -1Baniso -2Baniso -3
1--15.9663 Å20 Å240.62 Å2
2--3.2513 Å20 Å2
3---12.7151 Å2
Refine analyzeLuzzati coordinate error obs: 0.448 Å
Refinement stepCycle: 1 / Resolution: 3.3→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12600 0 57 107 12764
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113002HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0517782HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4300SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1883HARMONIC5
X-RAY DIFFRACTIONt_it13002HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion18.68
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_contact14688SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2859 259 5.31 %
Rwork0.26 4615 -
all0.2614 4874 -
obs--99.9 %

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