+Open data
-Basic information
Entry | Database: PDB / ID: 1iit | ||||||
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Title | GLUR0 LIGAND BINDING CORE COMPLEX WITH L-SERINE | ||||||
Components | Slr1257 protein | ||||||
Keywords | MEMBRANE PROTEIN / SAME FOLD AS PBPS | ||||||
Function / homology | Function and homology information kainate selective glutamate receptor complex / ligand-gated monoatomic ion channel activity / modulation of chemical synaptic transmission Similarity search - Function | ||||||
Biological species | Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Mayer, 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 |
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Remark 999 | SEQUENCE 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iit.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iit.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 1iit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iit_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 1iit_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 1iit_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 1iit_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/1iit ftp://data.pdbj.org/pub/pdb/validation_reports/ii/1iit | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25565.977 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: PCC6803 / Gene: slr1257, slr1257 GluR0 / Plasmid: pETGQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P73797 |
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#2: Chemical | ChemComp-SER / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.77 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 38% MPD, 0.2 M LiCl, 0.1 M Na Acetate, 10 mM L-Serine, 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
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97625 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 18810 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 20.29 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.69 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 19.3 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 131611 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | |||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.209 / Rfactor Rfree: 0.25 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.325 / Rfactor Rwork: 0.295 |