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- PDB-5hew: Pentameric ligand-gated ion channel ELIC mutant T28D -

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Basic information

Entry
Database: PDB / ID: 5hew
TitlePentameric ligand-gated ion channel ELIC mutant T28D
ComponentsGamma-aminobutyric-acid receptor subunit beta-1
KeywordsTRANSPORT PROTEIN / Pentameric ligand-gated ion channels / Membrane protein / Ligand-gated ion channel
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / membrane
Similarity search - Function
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
Similarity search - Domain/homology
Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsEngeler, S. / Dutzler, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Plos Biol. / Year: 2016
Title: Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels.
Authors: Bertozzi, C. / Zimmermann, I. / Engeler, S. / Hilf, R.J. / Dutzler, R.
History
DepositionJan 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1


Theoretical massNumber of molelcules
Total (without water)368,93010
Polymers368,93010
Non-polymers00
Water00
1
A: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1


Theoretical massNumber of molelcules
Total (without water)184,4655
Polymers184,4655
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23170 Å2
ΔGint-133 kcal/mol
Surface area66990 Å2
MethodPISA
2
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1


Theoretical massNumber of molelcules
Total (without water)184,4655
Polymers184,4655
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23000 Å2
ΔGint-132 kcal/mol
Surface area67260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.450, 266.960, 110.200
Angle α, β, γ (deg.)90.00, 110.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Gamma-aminobutyric-acid receptor subunit beta-1


Mass: 36892.984 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria)
Strain: 3937 / Gene: Dda3937_00520 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000 ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.603 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.603 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 33795 / % possible obs: 99.7 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.1
Reflection shellResolution: 4.5→4.6 Å / Redundancy: 1.6 % / Rmerge(I) obs: 1.892 / Mean I/σ(I) obs: 1.9 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YN6

2yn6


Resolution: 4.5→29.929 Å / SU ML: 0.75 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2707 1730 5.14 %
Rwork0.237 --
obs0.2387 33653 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.5→29.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25060 0 0 0 25060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325740
X-RAY DIFFRACTIONf_angle_d0.58435080
X-RAY DIFFRACTIONf_dihedral_angle_d13.09515060
X-RAY DIFFRACTIONf_chiral_restr0.0443890
X-RAY DIFFRACTIONf_plane_restr0.0044480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5001-4.6320.3672850.33652526X-RAY DIFFRACTION100
4.632-4.7810.25240.2962806X-RAY DIFFRACTION100
4.781-4.95110.33752690.28042501X-RAY DIFFRACTION100
4.9511-5.14840.3959200.26822774X-RAY DIFFRACTION100
5.1484-5.38140.32682430.26172551X-RAY DIFFRACTION100
5.3814-5.66330.2814450.24832756X-RAY DIFFRACTION100
5.6633-6.01550.3232250.24282559X-RAY DIFFRACTION100
6.0155-6.47560.2686640.25892775X-RAY DIFFRACTION100
6.4756-7.11930.32352070.26412586X-RAY DIFFRACTION100
7.1193-8.13140.3409810.24952740X-RAY DIFFRACTION100
8.1314-10.17730.21391290.20192683X-RAY DIFFRACTION100
10.1773-29.93010.21481580.21632666X-RAY DIFFRACTION99

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