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- PDB-4io5: Crystal Structure of the AvGluR1 ligand binding domain complex wi... -

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Basic information

Entry
Database: PDB / ID: 4io5
TitleCrystal Structure of the AvGluR1 ligand binding domain complex with alanine at 1.72 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
ALANINE / Glutamate receptor 1
Similarity search - Component
Biological speciesAdineta vaga (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.721 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: Source and taxonomy / Category: entity_src_gen
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

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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)55,37610
Polymers54,9852
Non-polymers3918
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-74 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.428, 100.691, 56.655
Angle α, β, γ (deg.)90.00, 116.44, 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-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17.5% 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 11, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→40 Å / Num. all: 58814 / Num. obs: 58814 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.1
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.5 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: dev_1039)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4IO2

4io2


Resolution: 1.721→29.51 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 1840 3.16 %Random
Rwork0.1585 ---
obs0.1597 58199 98.82 %-
all-58199 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.721→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 18 564 4356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113968
X-RAY DIFFRACTIONf_angle_d1.2755389
X-RAY DIFFRACTIONf_dihedral_angle_d10.6831483
X-RAY DIFFRACTIONf_chiral_restr0.074627
X-RAY DIFFRACTIONf_plane_restr0.006693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7209-1.76750.26751110.21274179X-RAY DIFFRACTION95
1.7675-1.81950.22531530.20344245X-RAY DIFFRACTION98
1.8195-1.87820.23951430.19264319X-RAY DIFFRACTION98
1.8782-1.94530.20321430.18154306X-RAY DIFFRACTION99
1.9453-2.02320.22891400.17724337X-RAY DIFFRACTION99
2.0232-2.11520.19851380.15554317X-RAY DIFFRACTION99
2.1152-2.22670.18021440.15034330X-RAY DIFFRACTION99
2.2267-2.36620.21231300.1484371X-RAY DIFFRACTION99
2.3662-2.54880.18351420.15394349X-RAY DIFFRACTION99
2.5488-2.80510.19191400.16224380X-RAY DIFFRACTION100
2.8051-3.21050.21271550.16224366X-RAY DIFFRACTION100
3.2105-4.04330.19331430.14374418X-RAY DIFFRACTION100
4.0433-29.51450.16311580.14854442X-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)
10.02510.00980.00880.01890.01660.01260.02730.0471-0.032-0.05990.02140.01610.0092-0.02970.06110.0764-0.0781-0.12490.0617-0.0724-0.0877-4.737938.1501-17.8385
20.2108-0.022-0.03590.1469-0.02360.29170.1313-0.0290.1317-0.06730.1115-0.1507-0.13170.09580.24990.0702-0.03850.02960.0806-0.06490.13324.857952.8472-5.3465
30.2211-0.0405-0.07190.14670.01880.31490.2087-0.02050.1826-0.03860.0991-0.0229-0.11230.06680.38050.0401-0.01760.14460.0978-0.05810.12756.835853.2384-8.3596
40.0063-0.0126-0.0080.03660.02560.01750.0261-0.00360.0022-0.040.043-0.0599-0.01310.06270.03370.0753-0.00190.01310.0809-0.01570.06558.36533.2023-10.4534
50.0240.0018-0.01160.05260.00120.00660.0237-0.00590.02250.0412-0.01180.0499-0.0017-0.0070.01720.13870.0628-0.03410.1428-0.02820.0599-1.728537.406620.7955
60.04890.0015-0.01760.1263-0.02290.08140.0001-0.0937-0.00910.14370.0412-0.0586-0.01760.01970.07120.09430.0256-0.00230.0925-0.00920.05632.537532.877415.8484
70.0347-0.0152-0.00720.01910.00120.0457-0.0764-0.0818-0.07830.0106-0.0323-0.0790.01730.0384-0.07180.09390.0449-0.01410.1136-0.00850.136716.387820.668610.1149
80.0041-0.002-0.00690.04980.00480.02980.0120.0004-0.00140.05870.0388-0.0504-0.02720.03430.05990.06210.0098-0.01040.0824-0.01850.06153.554842.343411.648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:64)
2X-RAY DIFFRACTION2(chain A and resid 65:133)
3X-RAY DIFFRACTION3(chain A and resid 134:222)
4X-RAY DIFFRACTION4(chain A and resid 223:248)
5X-RAY DIFFRACTION5(chain B and resid 1:25)
6X-RAY DIFFRACTION6(chain B and resid 26:117)
7X-RAY DIFFRACTION7(chain B and resid 118:203)
8X-RAY DIFFRACTION8(chain B and resid 204:248)

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