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- PDB-3tlt: The GLIC pentameric Ligand-Gated Ion Channel H11'F mutant in a lo... -

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Basic information

Entry
Database: PDB / ID: 3tlt
TitleThe GLIC pentameric Ligand-Gated Ion Channel H11'F mutant in a locally-closed conformation (LC1 subtype)
ComponentsGlr4197 protein
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / Cys-loop receptor family
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
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSauguet, L. / Nury, H. / Corringer, P.J. / Delarue, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A locally closed conformation of a bacterial pentameric proton-gated ion channel.
Authors: Prevost, M.S. / Sauguet, L. / Nury, H. / Van Renterghem, C. / Huon, C. / Poitevin, F. / Baaden, M. / Delarue, M. / Corringer, P.J.
History
DepositionAug 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)183,62311
Polymers182,9355
Non-polymers6886
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23050 Å2
ΔGint-202 kcal/mol
Surface area63040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.370, 129.020, 160.530
Angle α, β, γ (deg.)90.000, 102.140, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glr4197 protein / GLIC


Mass: 36587.066 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: H277F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 4.99 Å3/Da / Density % sol: 75.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4 / Details: pH 4, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.3→44.1 Å / Num. obs: 49209 / % possible obs: 91.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 79.19 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.046 / Net I/σ(I): 11.7
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2 / Num. unique all: 7339 / Rsym value: 0.31 / % possible all: 92.8

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.1data extraction
SCALAdata scaling
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→27.04 Å / Cor.coef. Fo:Fc: 0.8368 / Cor.coef. Fo:Fc free: 0.824 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.211 / SU Rfree Blow DPI: 0.399
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 2477 5.04 %RANDOM
Rwork0.2238 ---
obs0.2248 49174 90.8 %-
Displacement parametersBiso max: 219.89 Å2 / Biso mean: 114.671 Å2 / Biso min: 38.98 Å2
Baniso -1Baniso -2Baniso -3
1--19.0306 Å20 Å247.8136 Å2
2---18.1756 Å20 Å2
3---37.2062 Å2
Refine analyzeLuzzati coordinate error obs: 0.81 Å
Refinement stepCycle: LAST / Resolution: 3.3→27.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12630 0 17 29 12676
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4308SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1873HARMONIC5
X-RAY DIFFRACTIONt_it12992HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion1761SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact14855SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12992HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg17757HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion20.12
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2972 199 5.33 %
Rwork0.2878 3538 -
all0.2883 3737 -
obs--90.8 %

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