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Open data
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Basic information
Entry | Database: PDB / ID: 1us4 | ||||||
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Title | PUTATIVE GLUR0 LIGAND BINDING CORE WITH L-GLUTAMATE | ||||||
![]() | PUTATIVE GLUR0 LIGAND BINDING CORE | ||||||
![]() | RECEPTOR / MEMBRANE PROTEIN / GLUTAMATE RECEPTOR / GLUR0 / L-GLUTAMATE / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS | ||||||
Function / homology | TRAP transporter solute receptor, TAXI family / NMT1-like family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / GLUTAMIC ACID / Glutamate receptor![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tahirov, T.H. / Inagaki, E. / Takahashi, H. | ||||||
![]() | ![]() Title: Structure of the Thermus Thermophilus Putative Periplasmic Glutamate/Glutamine-Binding Protein Authors: Takahashi, H. / Inagaki, E. / Kuroishi, C. / Tahirov, T.H. | ||||||
History |
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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 viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.8 KB | Display | ![]() |
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PDB format | ![]() | 56.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.9 KB | Display | ![]() |
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Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 33723.168 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING CORE, RESIDUES 1-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GLU / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.88 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5 Details: VAPOUR DIFFUSION METHOD, 10 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH RESERVOIR SOLUTION (20.3% PEG4000, 0.09M SODIUM CITRATE PH 5.0) AND EQUILIBRATED AGAINST RESERVOIR SOLUTION AT ROOM ...Details: VAPOUR DIFFUSION METHOD, 10 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH RESERVOIR SOLUTION (20.3% PEG4000, 0.09M SODIUM CITRATE PH 5.0) AND EQUILIBRATED AGAINST RESERVOIR SOLUTION AT ROOM TEMPERATURE (291 K). CRYSTALS IN FORM OF PARALLELEPIPEDS WERE GROWN TO 0.05X0.05X0.15 MM WITHIN 10 DAYS. CRYOPROTECTANT CONTENT: 25% PEG4000, 18% ETHYLENE GLYCOL AND 0.1M SODIUM CITRATE PH 5.0. | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 15, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→50 Å / Num. obs: 28082 / % possible obs: 95.2 % / Observed criterion σ(I): -1 / Redundancy: 4.4 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 25.1 | ||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 13.6 / % possible all: 98 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 50 Å / Num. measured all: 123941 / Rmerge(I) obs: 0.067 | ||||||||||||
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 13.6 |
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Processing
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Refinement | Method to determine structure: ![]() Details: FRIEDEL PAIRS WERE INCLUDED FOR THE REFINEMENT OF ANOMALOUS CONTRIBUTION OF SE ATOMS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.815 Å2 / ksol: 0.343669 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→28.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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