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- PDB-3igq: Crystal structure of the extracellular domain of a bacterial pent... -

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Basic information

Entry
Database: PDB / ID: 3igq
TitleCrystal structure of the extracellular domain of a bacterial pentameric ligand-gated ion channel
ComponentsGlr4197 protein
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / pLGIC cys-loop
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
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 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / : / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsNury, H. / Delarue, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of the extracellular domain of a bacterial ligand-gated ion channel
Authors: Nury, H. / Bocquet, N. / Le Poupon, C. / Raynal, B. / Haouz, A. / Corringer, P.-J. / Delarue, M.
History
DepositionJul 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
F: Glr4197 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,15130
Polymers137,2366
Non-polymers1,91524
Water7,350408
1
A: Glr4197 protein
B: Glr4197 protein
C: Glr4197 protein
hetero molecules

A: Glr4197 protein
B: Glr4197 protein
C: Glr4197 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,15130
Polymers137,2366
Non-polymers1,91524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
2
D: Glr4197 protein
E: Glr4197 protein
F: Glr4197 protein
hetero molecules

D: Glr4197 protein
E: Glr4197 protein
F: Glr4197 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,15130
Polymers137,2366
Non-polymers1,91524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area34960 Å2
ΔGint-635 kcal/mol
Surface area87390 Å2
Unit cell
Length a, b, c (Å)84.450, 130.240, 113.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glr4197 protein


Mass: 22872.697 Da / Num. of mol.: 6
Fragment: extracellular N-terminal fragment, UNP residues 44-235
Mutation: F116G, Y119T, P120E, F121S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glr4197 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8

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Non-polymers , 5 types, 432 molecules

#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.28 Å3/Da / Density % sol: 45.96 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 108138 / Num. obs: 105975 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.03 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.23
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.01 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.96 / % possible all: 97.91

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.36 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.Friedel's pair are not merged during data collection (the anomalous information from the mercury ions were used), while the refinement ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.Friedel's pair are not merged during data collection (the anomalous information from the mercury ions were used), while the refinement is made with merged plus and minus reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.25515 2845 5.1 %RANDOM
Rwork0.2066 ---
obs0.20902 53353 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.431 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2--1.07 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8603 0 42 408 9053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228812
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.97311997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62151060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29123.883412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.173151481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0821573
X-RAY DIFFRACTIONr_chiral_restr0.1130.21403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216651
X-RAY DIFFRACTIONr_mcbond_it1.111.55422
X-RAY DIFFRACTIONr_mcangle_it2.21228867
X-RAY DIFFRACTIONr_scbond_it3.17633390
X-RAY DIFFRACTIONr_scangle_it5.5814.53130
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A623tight positional0.10.05
B623tight positional0.070.05
C623tight positional0.090.05
D623tight positional0.10.05
E623tight positional0.090.05
F623tight positional0.090.05
A628medium positional0.120.5
B628medium positional0.090.5
C628medium positional0.110.5
D628medium positional0.190.5
E628medium positional0.120.5
F628medium positional0.140.5
A623tight thermal0.220.5
B623tight thermal0.220.5
C623tight thermal0.190.5
D623tight thermal0.220.5
E623tight thermal0.230.5
F623tight thermal0.240.5
A628medium thermal0.22
B628medium thermal0.22
C628medium thermal0.212
D628medium thermal0.192
E628medium thermal0.212
F628medium thermal0.212
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 215 -
Rwork0.25 3861 -
obs--99.76 %

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