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- PDB-4y9a: Crystal structure of Triosephosphate Isomerase from Streptomyces ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4y9a | |||||||||
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Title | Crystal structure of Triosephosphate Isomerase from Streptomyces coelicolor | |||||||||
![]() | Triosephosphate isomerase | |||||||||
![]() | ISOMERASE / TIM Barrel / TPI | |||||||||
Function / homology | ![]() triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Romero-Romero, S. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins. Authors: Romero-Romero, S. / Costas, M. / Rodriguez-Romero, A. / Alejandro Fernandez-Velasco, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.3 KB | Display | ![]() |
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PDB format | ![]() | 162.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450 KB | Display | ![]() |
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Full document | ![]() | 460.9 KB | Display | |
Data in XML | ![]() | 38.4 KB | Display | |
Data in CIF | ![]() | 53.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y8fC ![]() 4y90C ![]() 4y96C ![]() 3ta6S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | Dimer by Gel Filtration |
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Components
#1: Protein | Mass: 28053.775 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Expression tag: GSH / Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS hydrochloride pH 8.5, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 13, 2014 |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→43.03 Å / Num. obs: 43475 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 32.68 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TA6 Resolution: 2.294→39.634 Å / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.5 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.294→39.634 Å
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Refine LS restraints |
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LS refinement shell |
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