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Yorodumi- PDB-4y9a: Crystal structure of Triosephosphate Isomerase from Streptomyces ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y9a | |||||||||
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Title | Crystal structure of Triosephosphate Isomerase from Streptomyces coelicolor | |||||||||
Components | Triosephosphate isomerase | |||||||||
Keywords | ISOMERASE / TIM Barrel / TPI | |||||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | |||||||||
Biological species | Streptomyces coelicolor (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.294 Å | |||||||||
Authors | Romero-Romero, S. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A. | |||||||||
Funding support | Mexico, 2items
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Citation | Journal: Phys Chem Chem Phys / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y9a.cif.gz | 202.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y9a.ent.gz | 162.2 KB | Display | PDB format |
PDBx/mmJSON format | 4y9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/4y9a ftp://data.pdbj.org/pub/pdb/validation_reports/y9/4y9a | HTTPS FTP |
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-Related structure data
Related structure data | 4y8fC 4y90C 4y96C 3ta6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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 |
-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.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / M145 / Gene: tpiA, tpi, SCO1945, SCC54.05c / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9Z520, triose-phosphate isomerase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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