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- PDB-2vl0: X-ray structure of a pentameric ligand gated ion channel from Erw... -

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Basic information

Entry
Database: PDB / ID: 2vl0
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC)
ComponentsCys-loop ligand-gated ion channel
KeywordsMEMBRANE PROTEIN / PENTAMERIC LIGAND GATED ION CHANNEL / PROKARYOTIC CYS-LOOP RECEPTOR / CATION SELECTIVE CHANNEL
Function / homology
Function and homology information


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 / 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 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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
Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.3 Å
AuthorsHilf, R.J.C. / Dutzler, R.
CitationJournal: Nature / Year: 2008
Title: X-Ray Structure of a Prokaryotic Pentameric Ligand-Gated Ion Channel
Authors: Hilf, R.J.C. / Dutzler, R.
History
DepositionJan 7, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_database_status / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cys-loop ligand-gated ion channel
B: Cys-loop ligand-gated ion channel
C: Cys-loop ligand-gated ion channel
D: Cys-loop ligand-gated ion channel
E: Cys-loop ligand-gated ion channel
F: Cys-loop ligand-gated ion channel
G: Cys-loop ligand-gated ion channel
H: Cys-loop ligand-gated ion channel
I: Cys-loop ligand-gated ion channel
J: Cys-loop ligand-gated ion channel


Theoretical massNumber of molelcules
Total (without water)368,21910
Polymers368,21910
Non-polymers00
Water00
1
A: Cys-loop ligand-gated ion channel
B: Cys-loop ligand-gated ion channel
C: Cys-loop ligand-gated ion channel
D: Cys-loop ligand-gated ion channel
E: Cys-loop ligand-gated ion channel


Theoretical massNumber of molelcules
Total (without water)184,1105
Polymers184,1105
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27910 Å2
ΔGint-183 kcal/mol
Surface area78630 Å2
MethodPQS
2
F: Cys-loop ligand-gated ion channel
G: Cys-loop ligand-gated ion channel
H: Cys-loop ligand-gated ion channel
I: Cys-loop ligand-gated ion channel
J: Cys-loop ligand-gated ion channel


Theoretical massNumber of molelcules
Total (without water)184,1105
Polymers184,1105
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27540 Å2
ΔGint-189 kcal/mol
Surface area81310 Å2
MethodPQS
Unit cell
Length a, b, c (Å)105.502, 266.147, 110.851
Angle α, β, γ (deg.)90.00, 109.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.31531, -0.93743, 0.14767), (0.9115, 0.34247, 0.22777), (-0.26409, 0.06279, 0.96245)-105.2138, 76.83292, -26.39396
2given(-0.79192, -0.61007, -0.0259), (0.5423, -0.72218, 0.42938), (-0.28066, 0.32599, 0.90275)-214.24937, 1.3117, -19.29384
3given(-0.80138, 0.52891, -0.27938), (-0.59737, -0.73164, 0.3284), (-0.03071, 0.43006, 0.90228)-177.44312, -122.39538, 11.27652
4given(0.30247, 0.91459, -0.26841), (-0.94172, 0.33025, 0.06407), (0.14724, 0.23338, 0.96117)-45.32915, -124.42756, 23.84669
5given(-0.04145, -0.00104, 0.99914), (0.06028, 0.99818, 0.00354), (-0.99732, 0.06037, -0.04131)-40.67315, -60.66836, -138.97089
6given(-0.27955, 0.09816, 0.9551), (0.92615, 0.28986, 0.24129), (-0.25316, 0.95202, -0.17194)-63.25872, 9.65004, -28.85288
7given(-0.2531, 0.35393, 0.90038), (0.49371, -0.75312, 0.43482), (0.83198, 0.55457, 0.01587)-51.88315, -71.91399, 75.48394
8given(0.00825, 0.41354, 0.91045), (-0.64063, -0.69691, 0.32235), (0.7678, -0.58592, 0.25917)-21.48747, -192.76185, 30.55765
9given(0.13625, -0.92339, -0.35886), (0.18847, 0.37978, -0.90567), (0.97258, 0.05577, 0.22578)-208.07477, -18.27176, 48.22716

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Components

#1: Protein
Cys-loop ligand-gated ion channel / ELIC


Mass: 36821.949 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Plasmid: PET26 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C7B7

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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: 4.19 Å3/Da / Density % sol: 65 %
Description: PHASES WERE EXTENDED BY CYCLIC 10-FOLD NCS AVERAGING
Crystal growpH: 6.5
Details: 15 % PEG 4000, 200MM AMMONIUM SULFATE, 50 MM ADA PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979
DetectorType: DECTRIS CUSTOM / Date: Sep 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 86136 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 21 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.4
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 15.1 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
SHELXC Dphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 3.3→29.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4877940.57 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELYHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 4335 5 %THIN RESOLUTION SLICES
Rwork0.263 ---
obs0.263 86080 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.2833 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 129.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å20 Å220.43 Å2
2---23.24 Å20 Å2
3---19.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a1.14 Å1.2 Å
Refinement stepCycle: LAST / Resolution: 3.3→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25010 0 0 0 25010
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.62
X-RAY DIFFRACTIONc_mcangle_it2.63
X-RAY DIFFRACTIONc_scbond_it2.82.5
X-RAY DIFFRACTIONc_scangle_it4.24
Refine LS restraints NCSNCS model details: TIGHT NCS POSITIONAL AND B-FACTOR RESTRAINTS
Weight Biso : 5 / Weight position: 100
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.44 672 4.7 %
Rwork0.435 13631 -
obs--100 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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