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- PDB-3ehz: X-ray structure of the pentameric ligand gated ion channel of Glo... -

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Basic information

Entry
Database: PDB / ID: 3ehz
TitleX-ray structure of the pentameric ligand gated ion channel of Gloebacter violaceus (GLIC) in a presumptive open conformation
ComponentsGlr4197 protein
KeywordsMEMBRANE PROTEIN / pentameric ligand gated ion channel / prokaryotic cys-loop receptor / cation selective channel
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium 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 / molecular replacement / Resolution: 3.1 Å
AuthorsHilf, R.J.C. / Dutzler, R.
CitationJournal: Nature / Year: 2008
Title: Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel
Authors: Hilf, R.J. / Dutzler, R.
History
DepositionSep 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_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: Glr4197 protein
B: Glr4197 protein
C: Glr4197 protein
D: Glr4197 protein
E: Glr4197 protein


Theoretical massNumber of molelcules
Total (without water)181,3895
Polymers181,3895
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21070 Å2
ΔGint-140.2 kcal/mol
Surface area65230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.225, 132.864, 161.422
Angle α, β, γ (deg.)90.000, 102.190, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

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: 8 - 317

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE

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Components

#1: Protein
Glr4197 protein


Mass: 36277.723 Da / Num. of mol.: 5 / Fragment: UNP residues 50-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7NDN8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 5.28 Å3/Da / Density % sol: 76.72 % / Mosaicity: 0.64 °
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 9% PEG4000, 50mM CH3COONa, 200mM (NH4)2SO4, pH4.0, vapor diffusion, hanging drop, temperature 277.15K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 66826 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 5.28
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.276.50.6071.16285197310.60799.9
3.27-3.476.50.3751.95986192200.37599.9
3.47-3.716.10.23235276486240.23299.2
3.71-460.1454876080650.1499.5
4-4.386.60.0917.34871873980.09199.6
4.38-4.96.20.06494175167220.06499.5
4.9-5.666.30.0619.53770959640.06199.8
5.66-6.936.40.06210.43256850580.06299.8
6.93-9.85.90.04910.32308238800.04999.3
9.8-48.855.80.03710.11251921640.03798

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL0

2vl0


Resolution: 3.1→19.972 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.746 / SU ML: 0.47 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 3347 5.03 %
Rwork0.238 --
obs0.239 66589 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.742 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 185.65 Å2 / Biso mean: 87.014 Å2 / Biso min: 28.52 Å2
Baniso -1Baniso -2Baniso -3
1-15.725 Å2-0 Å2-38.313 Å2
2---5.804 Å2-0 Å2
3----9.92 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12605 0 0 47 12652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112945
X-RAY DIFFRACTIONf_angle_d1.37817685
X-RAY DIFFRACTIONf_chiral_restr0.0912060
X-RAY DIFFRACTIONf_plane_restr0.0052215
X-RAY DIFFRACTIONf_dihedral_angle_d21.0174550
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2521X-RAY DIFFRACTIONPOSITIONAL
12B2521X-RAY DIFFRACTIONPOSITIONAL0.032
13C2521X-RAY DIFFRACTIONPOSITIONAL0.028
14D2521X-RAY DIFFRACTIONPOSITIONAL0.036
15E2521X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.14410.38321970.33762533X-RAY DIFFRACTION100
3.1441-3.19090.379620.31382722X-RAY DIFFRACTION100
3.1909-3.24060.31621340.32062614X-RAY DIFFRACTION100
3.2406-3.29340.4181970.33232596X-RAY DIFFRACTION100
3.2934-3.350.2981340.31662622X-RAY DIFFRACTION100
3.35-3.41060.40351130.31332680X-RAY DIFFRACTION100
3.4106-3.47590.39241240.30552641X-RAY DIFFRACTION100
3.4759-3.54640.37291800.28242534X-RAY DIFFRACTION99
3.5464-3.62310.29451390.25842639X-RAY DIFFRACTION99
3.6231-3.70690.2971650.24442701X-RAY DIFFRACTION99
3.7069-3.7990.26521550.23172579X-RAY DIFFRACTION99
3.799-3.90090.28611870.22952592X-RAY DIFFRACTION100
3.9009-4.01480.33521540.23852625X-RAY DIFFRACTION100
4.0148-4.14330.2268360.22082735X-RAY DIFFRACTION99
4.1433-4.290.24271800.20452610X-RAY DIFFRACTION100
4.29-4.45990.23671860.19172586X-RAY DIFFRACTION100
4.4599-4.66040.17921790.17142588X-RAY DIFFRACTION100
4.6604-4.90270.12940.14852744X-RAY DIFFRACTION99
4.9027-5.20480.19481860.162609X-RAY DIFFRACTION100
5.2048-5.59840.22161810.19412634X-RAY DIFFRACTION100
5.5984-6.14690.27391870.2372596X-RAY DIFFRACTION100
6.1469-7.002600.24382797X-RAY DIFFRACTION99
7.0026-8.69940.2931800.22082605X-RAY DIFFRACTION99
8.6994-19.97240.1751870.23012660X-RAY DIFFRACTION99

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