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- PDB-4lmj: GLIC Liganded-closed-channel Conformation, Mutant T25'A -

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Basic information

Entry
Database: PDB / ID: 4lmj
TitleGLIC Liganded-closed-channel Conformation, Mutant 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: 3.44 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _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
E: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
A: Proton-gated ion channel
D: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,47716
Polymers181,6745
Non-polymers80311
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23400 Å2
ΔGint-236 kcal/mol
Surface area65240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.120, 134.320, 159.890
Angle α, β, γ (deg.)90.00, 101.96, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain E and (resseq 7:316 )
21chain B and (resseq 7:316 )
31chain C and (resseq 7:316 )
41chain A and (resseq 7:316 )
51chain D and (resseq 7:316 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 7 - 316 / Label seq-ID: 9 - 318

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'E' and (resseq 7:316 )EA
2chain 'B' and (resseq 7:316 )BB
3chain 'C' and (resseq 7:316 )CC
4chain 'A' and (resseq 7:316 )AD
5chain 'D' and (resseq 7:316 )DE

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Components

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


Mass: 36334.781 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: 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
#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: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na

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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: 5.24 Å3/Da / Density % sol: 76.5 %
Description: RPIM = 0.095 (0.453 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 / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2012
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.44→49.04 Å / Num. obs: 41437 / % possible obs: 98.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 51.8 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.7
Reflection shellResolution: 3.44→3.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.4 / % possible all: 92.7

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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: 3.44→49.038 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 0.12 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 1647 4.14 %
Rwork0.2269 --
obs0.228 39737 79.66 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.3174 Å2
Refinement stepCycle: LAST / Resolution: 3.44→49.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12595 0 22 0 12617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212946
X-RAY DIFFRACTIONf_angle_d1.44117680
X-RAY DIFFRACTIONf_dihedral_angle_d15.7434629
X-RAY DIFFRACTIONf_chiral_restr0.0982055
X-RAY DIFFRACTIONf_plane_restr0.0062215
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11E2519X-RAY DIFFRACTIONTORSIONAL0.065
12B2519X-RAY DIFFRACTIONTORSIONAL0.065
13C2519X-RAY DIFFRACTIONTORSIONAL0.063
14A2519X-RAY DIFFRACTIONTORSIONAL0.048
15D2519X-RAY DIFFRACTIONTORSIONAL0.038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4401-3.54130.335640.29431555X-RAY DIFFRACTION39
3.5413-3.65550.3087880.2812046X-RAY DIFFRACTION52
3.6555-3.78610.32951070.27692445X-RAY DIFFRACTION61
3.7861-3.93770.30191240.24822818X-RAY DIFFRACTION71
3.9377-4.11680.2721390.24483107X-RAY DIFFRACTION79
4.1168-4.33370.22731510.21393472X-RAY DIFFRACTION87
4.3337-4.60510.25441580.19873541X-RAY DIFFRACTION90
4.6051-4.96030.21711530.16483664X-RAY DIFFRACTION92
4.9603-5.45890.20231650.18323751X-RAY DIFFRACTION94
5.4589-6.24740.27121610.22513810X-RAY DIFFRACTION95
6.2474-7.86590.24111660.25543902X-RAY DIFFRACTION97
7.8659-49.04270.25391710.24873979X-RAY DIFFRACTION98

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