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- PDB-1h1y: The structure of the cytosolic D-ribulose-5-phosphate 3-epimerase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h1y | ||||||
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Title | The structure of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice complexed with sulfate | ||||||
![]() | D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE | ||||||
![]() | ISOMERASE / 3-EPIMERASE / OXIDATIVE PENTOSE PHOSPHATE PATHWAY | ||||||
Function / homology | ![]() ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jelakovic, S. / Schulz, G.E. | ||||||
![]() | ![]() Title: Structure and Catalytic Mechanism of the Cytosolic D-Ribulose-5-Phosphate 3-Epimerase from Rice Authors: Jelakovic, S. / Kopriva, S. / Suss, K. / Schulz, G.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.8 KB | Display | ![]() |
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PDB format | ![]() | 78.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.8 KB | Display | ![]() |
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Full document | ![]() | 435.2 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 33.5 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.894186, 0.163495, 0.416775), Vector: |
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Components
#1: Protein | Mass: 24316.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | CATALYSES INTERCONVERSION BETWEEN D-RIBULOSE 5-PHOSPHATE AND D-XYLULOSE 5-PHOSPHATE. COMPONENT OF ...CATALYSES INTERCONVE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→29 Å / Num. obs: 42044 / % possible obs: 98 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.021 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 29 Å / % possible obs: 98 % |
Reflection shell | *PLUS % possible obs: 98 % / Redundancy: 4.3 % / Num. unique obs: 5730 / Rmerge(I) obs: 0.042 / Mean I/σ(I) obs: 16 |
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Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.87→25 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 29 Å / % reflection Rfree: 3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |