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- PDB-1ii5: CRYSTAL STRUCTURE OF THE GLUR0 LIGAND BINDING CORE COMPLEX WITH L... -

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Basic information

Entry
Database: PDB / ID: 1ii5
TitleCRYSTAL STRUCTURE OF THE GLUR0 LIGAND BINDING CORE COMPLEX WITH L-GLUTAMATE
ComponentsSlr1257 protein
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / membrane
Similarity search - Function
Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Potassium channel domain / Ion channel / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II ...Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Potassium channel domain / Ion channel / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Slr1257 protein
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsMayer, M.L. / Olson, R. / Gouaux, E.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Mechanisms for ligand binding to GluR0 ion channels: crystal structures of the glutamate and serine complexes and a closed apo state.
Authors: Mayer, M.L. / Olson, R. / Gouaux, E.
#1: Journal: Nature / Year: 1999
Title: FUNCTIONAL CHARACTERIZATION OF A POTASSIUM-SELECTIVE PROKARYOTIC GLUTAMATE RECEPTOR
Authors: CHEN, G.-Q. / CUI, C. / MAYER, M.L. / GOUAUX, E.
History
DepositionApr 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 11, 2012Group: Database references
Revision 1.4Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 999SEQUENCE NATIVE GLURO IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED BY THE AUTHOR IS THE ...SEQUENCE NATIVE GLURO IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED BY THE AUTHOR IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLURO. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A THR LINKER. THE SEQUENCE, AS A RESULT, MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Slr1257 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8412
Polymers25,6941
Non-polymers1471
Water2,414134
1
A: Slr1257 protein
hetero molecules

A: Slr1257 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6824
Polymers51,3882
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Unit cell
Length a, b, c (Å)97.866, 49.706, 55.572
Angle α, β, γ (deg.)90.0, 116.84, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Slr1257 protein


Mass: 25694.107 Da / Num. of mol.: 1
Fragment: GluR0 ligand binding core, residues 44-140, 256-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / Gene: GluR0 slr1257, slr1257 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P73797
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 38% MPD, 100 mM sodium acetate, 10 mM L-glutamic acid, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / PH range low: 4.8 / PH range high: 4.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 mg/mlprotein1drop
234-38 %MPD1reservoir
3100 mMsodium acetate1reservoir
410 mML-glutamate1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 31427 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 8.4 / Num. unique all: 3130 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 179108
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassification
SOLVEphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 1548 RANDOM
Rwork0.216 --
all0.245 31427 -
obs0.244 31315 -
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1660 0 10 134 1804
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.259
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_improper_angle_d1.24
LS refinement shellResolution: 1.6→1.67 Å
RfactorNum. reflection
Rfree0.377 177
Rwork0.334 -
obs-3782
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.24
LS refinement shell
*PLUS
Rfactor Rfree: 0.377 / Rfactor Rwork: 0.334

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