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- PDB-4lml: GLIC double mutant I9'A T25'A -

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Basic information

Entry
Database: PDB / ID: 4lml
TitleGLIC double mutant I9'A T25'A
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / pentameric ligand-gated ion channel / membrane protein / prokaryotic CYS-loop receptor
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: 3.8 Å
AuthorsGrosman, C. / Gonzalez-Gutierrez, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography.
Authors: Gonzalez-Gutierrez, G. / Cuello, L.G. / Nair, S.K. / Grosman, C.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)181,4645
Polymers181,4645
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20530 Å2
ΔGint-135 kcal/mol
Surface area66110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.803, 127.997, 190.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain E) / NCS domain segments: (Selection details: chain 'E')

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Components

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


Mass: 36292.703 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: I275A,T291A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glvI, glr4197 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7NDN8

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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: 4.12 Å3/Da / Density % sol: 70.16 %
Description: RPIM = 0.06 (0.337 FOR HIGHEST RESOLUTION SHELL)
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 10-12% PEG4000, 225 mM ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.8→44.12 Å / Num. obs: 24202 / % possible obs: 97.2 % / Redundancy: 14 % / Biso Wilson estimate: 24.05 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 12
Reflection shellHighest resolution: 3.8 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.239 / Mean I/σ(I) obs: 1.9 / % possible all: 92

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EHZ

3ehz


Resolution: 3.8→38.932 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.54 / σ(F): 0 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3017 1824 8.36 %
Rwork0.2463 --
obs0.2509 21810 72.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.19 Å2 / Biso mean: 53.4301 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: LAST / Resolution: 3.8→38.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12580 0 0 0 12580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712920
X-RAY DIFFRACTIONf_angle_d1.22217650
X-RAY DIFFRACTIONf_chiral_restr0.0492050
X-RAY DIFFRACTIONf_plane_restr0.0062215
X-RAY DIFFRACTIONf_dihedral_angle_d15.9424610
Refine LS restraints NCSNumber: 7427 / Type: POSITIONAL / Rms dev position: 6.174 Å
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8-3.90280.3377830.3224925100844
3.9028-4.01750.45111050.27951043114850
4.0175-4.1470.31881030.26961121122454
4.147-4.29510.29961030.23771277138061
4.2951-4.46680.28691320.22771337146964
4.4668-4.66980.25511370.22241429156668
4.6698-4.91550.26281360.20041547168373
4.9155-5.22280.23581340.21562169674
5.2228-5.6250.3261610.21991635179678
5.625-6.1890.33941590.23791786194583
6.189-7.07990.29471860.25231991217793
7.0799-8.90230.31651890.27062100228997
8.9023-38.93440.28641960.26942233242998

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