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- PDB-2ou4: Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ou4 | ||||||
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Title | Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii | ||||||
![]() | D-tagatose 3-epimerase | ||||||
![]() | ISOMERASE / BETA/ALPHA BARREL | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoshida, H. / Yamada, M. / Nishitani, T. / Takada, G. / Izumori, K. / Kamitori, S. | ||||||
![]() | ![]() Title: Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose Authors: Yoshida, H. / Yamada, M. / Nishitani, T. / Takada, G. / Izumori, K. / Kamitori, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 239.1 KB | Display | ![]() |
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PDB format | ![]() | 192.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.7 KB | Display | ![]() |
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Full document | ![]() | 480.3 KB | Display | |
Data in XML | ![]() | 48.9 KB | Display | |
Data in CIF | ![]() | 69.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qulC ![]() 2qumC ![]() 2qunC ![]() 2hk0S S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 32657.404 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O50580, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 10000, 0.1M HEPES, 0.01M strontium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 44731 / Num. obs: 44731 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.68 / Num. unique all: 4440 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HK0 Resolution: 2.5→42.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 41062.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.692 Å2 / ksol: 0.402173 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→42.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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