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- PDB-3tlv: The GLIC pentameric Ligand-Gated Ion Channel Loop2-22' oxidized m... -

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Basic information

Entry
Database: PDB / ID: 3tlv
TitleThe GLIC pentameric Ligand-Gated Ion Channel Loop2-22' oxidized mutant in a locally-closed conformation (LC3 subtype)
ComponentsGlr4197 protein
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / Cys-loop receptor family
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / 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
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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)183,31711
Polymers182,6305
Non-polymers6886
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23070 Å2
ΔGint-204 kcal/mol
Surface area64770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.140, 127.756, 160.866
Angle α, β, γ (deg.)90.000, 101.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glr4197 protein / GLIC


Mass: 36525.922 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: C69S/K75C/L288C
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: 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
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 4.94 Å3/Da / Density % sol: 75.09 %
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: ESRF / Beamline: ID29
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→49.23 Å / Num. obs: 78570 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 80.19 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.042 / Net I/σ(I): 13
Reflection shellResolution: 2.9→3.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2 / Num. unique all: 11073 / Rsym value: 0.395 / % possible all: 96.5

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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: 2.9→49.23 Å / Cor.coef. Fo:Fc: 0.8401 / Cor.coef. Fo:Fc free: 0.8366 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.387 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.267
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3932 5.01 %RANDOM
Rwork0.2155 ---
obs0.2161 78555 99.78 %-
Displacement parametersBiso max: 184.35 Å2 / Biso mean: 78.0608 Å2 / Biso min: 30.16 Å2
Baniso -1Baniso -2Baniso -3
1--11.8999 Å20 Å233.4475 Å2
2--0.3558 Å20 Å2
3---11.5441 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12600 0 17 105 12722
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4284SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes265HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1870HARMONIC5
X-RAY DIFFRACTIONt_it12961HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion1760SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact15045SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12961HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17725HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion19.15
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3058 270 4.74 %
Rwork0.2621 5426 -
all0.2641 5696 -
obs--99.78 %

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