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- PDB-4io4: Crystal Structure of the AvGluR1 ligand binding domain complex wi... -

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Basic information

Entry
Database: PDB / ID: 4io4
TitleCrystal Structure of the AvGluR1 ligand binding domain complex with serine at 1.94 Angstrom resolution
ComponentsAvGluR1 ligand binding domain
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / G protein-coupled receptor activity / postsynaptic membrane / cell surface receptor signaling pathway
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / GPCR, family 3 / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / GPCR, family 3 / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SERINE / Glutamate receptor 1
Similarity search - Component
Biological speciesAdineta vaga (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 Å
AuthorsLomash, S. / Chittori, S. / Mayer, M.L.
CitationJournal: Structure / Year: 2013
Title: Anions Mediate Ligand Binding in Adineta vaga Glutamate Receptor Ion Channels.
Authors: Lomash, S. / Chittori, S. / Brown, P. / Mayer, M.L.
History
DepositionJan 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
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_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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AvGluR1 ligand binding domain
B: AvGluR1 ligand binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,62713
Polymers54,9852
Non-polymers64311
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-83 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.357, 100.279, 59.890
Angle α, β, γ (deg.)90.00, 117.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AvGluR1 ligand binding domain


Mass: 27492.455 Da / Num. of mol.: 2 / Fragment: unp residues 457-567; 680-812
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adineta vaga (invertebrata) / Plasmid: pet22B modified / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: E9P5T5
#2: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF AvGluR1. TRANSMEMBRANE ...THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF AvGluR1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (457-567 AND 680-812)

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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: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.1 M NaCitrate, 0.1 M BisTris Propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→40 Å / Num. all: 43189 / Num. obs: 43189 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 27.4
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Io2

4io2


Resolution: 1.941→35.062 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1833 2154 5.05 %Random
Rwork0.1448 ---
obs0.1468 42665 99.58 %-
all-42665 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.941→35.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 33 262 4094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124089
X-RAY DIFFRACTIONf_angle_d1.2995564
X-RAY DIFFRACTIONf_dihedral_angle_d12.531548
X-RAY DIFFRACTIONf_chiral_restr0.071643
X-RAY DIFFRACTIONf_plane_restr0.006721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9414-1.98650.23371230.19132531X-RAY DIFFRACTION94
1.9865-2.03620.23061310.18442701X-RAY DIFFRACTION100
2.0362-2.09120.24761290.17652719X-RAY DIFFRACTION100
2.0912-2.15280.22171250.15722720X-RAY DIFFRACTION100
2.1528-2.22220.18511430.14922733X-RAY DIFFRACTION100
2.2222-2.30170.19431450.1432710X-RAY DIFFRACTION100
2.3017-2.39380.18981600.14712678X-RAY DIFFRACTION100
2.3938-2.50270.20331480.15322699X-RAY DIFFRACTION100
2.5027-2.63460.20371480.14292688X-RAY DIFFRACTION100
2.6346-2.79960.19341610.1512716X-RAY DIFFRACTION100
2.7996-3.01570.20151480.16112697X-RAY DIFFRACTION100
3.0157-3.31890.18291410.14962730X-RAY DIFFRACTION100
3.3189-3.79870.17591770.13732695X-RAY DIFFRACTION100
3.7987-4.7840.14431290.11342723X-RAY DIFFRACTION100
4.784-35.06750.17131460.15122771X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.8777-0.6894-0.94432.5273-2.24732.69320.06490.1317-0.1475-0.40740.05130.03340.0564-0.0014-0.10250.2768-0.03070.04430.213-0.00740.15013.968231.0094-20.6422
22.03611.217-0.01532.30.10771.1023-0.02980.21840.035-0.18760.1790.0624-0.04610.018-0.14610.20420.0090.00510.17070.04380.18020.721127.2536-11.6915
32.76020.04970.8033.6639-0.1032.22180.02120.0407-0.1750.02960.0730.32490.1155-0.2432-0.09050.1798-0.0519-0.00360.22850.05890.318-11.861512.6167-8.0856
41.51830.72920.9493.93320.53273.3417-0.0396-0.16180.178-0.06210.06980.0755-0.1996-0.2280.00570.17420.00370.04330.15890.04960.1862-2.287435.9842-8.214
52.62210.83590.23782.9838-0.50812.68350.0897-0.4208-0.06760.19240.0574-0.240.21780.153-0.10590.28840.0693-0.01980.36830.07370.15310.631832.230622.5094
63.3841-0.79610.50372.1636-0.21551.5067-0.0131-0.32610.01640.12750.10110.04030.07680.0402-0.08170.2030.02790.01770.1750.01950.1666-0.980740.299312.8478
74.5232-2.61020.25844.68720.03371.0320.0395-0.13210.33340.01560.0050.2228-0.0798-0.1554-0.05620.2160.01380.01140.2146-0.01320.2161-12.4148.41659.8326
83.1994-1.4071-2.72952.5051.35112.8599-0.14480.136-0.24840.18670.06510.42910.3231-0.39610.11290.2759-0.00340.03110.30020.12930.3107-8.423526.381813.0306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:33)
2X-RAY DIFFRACTION2(chain A and resid 34:117)
3X-RAY DIFFRACTION3(chain A and resid 118:203)
4X-RAY DIFFRACTION4(chain A and resid 204:248)
5X-RAY DIFFRACTION5(chain B and resid 1:49)
6X-RAY DIFFRACTION6(chain B and resid 50:116)
7X-RAY DIFFRACTION7(chain B and resid 117:219)
8X-RAY DIFFRACTION8(chain B and resid 220:248)

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