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Yorodumi- PDB-4y90: Crystal structure of Triosephosphate Isomerase from Deinococcus r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y90 | |||||||||
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Title | Crystal structure of Triosephosphate Isomerase from Deinococcus radiodurans | |||||||||
Components | Triosephosphate isomerase | |||||||||
Keywords | ISOMERASE / TIM Barrel / TPI | |||||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | |||||||||
Biological species | Deinococcus radiodurans (radioresistant) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Romero-Romero, S. / Rodriguez-Romero, A. / Fernadez-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 | 4y90.cif.gz | 547 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y90.ent.gz | 461.3 KB | Display | PDB format |
PDBx/mmJSON format | 4y90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y90_validation.pdf.gz | 471.4 KB | Display | wwPDB validaton report |
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Full document | 4y90_full_validation.pdf.gz | 473.4 KB | Display | |
Data in XML | 4y90_validation.xml.gz | 44 KB | Display | |
Data in CIF | 4y90_validation.cif.gz | 64.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/4y90 ftp://data.pdbj.org/pub/pdb/validation_reports/y9/4y90 | HTTPS FTP |
-Related structure data
Related structure data | 4y8fC 4y96C 4y9aC 1yyaS 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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Components on special symmetry positions |
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Details | Dimer by Gel Filtration |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 25618.809 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Expression tag: GSH Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: DSM 20539 / JCM 16871 / Gene: tpiA, DR_1339 / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9RUP5, triose-phosphate isomerase |
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-Non-polymers , 5 types, 854 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.53 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.8 M ammonium sulfate, 0.1 M sodium citrate tribasic pH 5.6, 0.2 M potassium sodium tartrate |
-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: Mar 4, 2013 |
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: 2.1→36.133 Å / Num. obs: 64962 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 22.73 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.9 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YYA Resolution: 2.1→36.133 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.86 / Stereochemistry target values: ML
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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: 25.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→36.133 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -42.3282 Å / Origin y: 122.2282 Å / Origin z: 218.2869 Å
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Refinement TLS group | Selection details: all |