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- PDB-3vnk: Crystal structures of D-Psicose 3-epimerase with D-fructose from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vnk | ||||||
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Title | Crystal structures of D-Psicose 3-epimerase with D-fructose from Clostridium cellulolyticum H10 | ||||||
![]() | Xylose isomerase domain protein TIM barrel | ||||||
![]() | ISOMERASE / D-Psicose 3-epimerase / ketohexose / TIM barrrel | ||||||
Function / homology | ![]() D-psicose 3-epimerase / racemase and epimerase activity, acting on carbohydrates and derivatives / cobalt ion binding / manganese ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chan, H.C. / Zhu, Y. / Hu, Y. / Ko, T.P. / Huang, C.H. / Ren, F. / Chen, C.C. / Guo, R.T. / Sun, Y. | ||||||
![]() | ![]() Title: Crystal structures of D-psicose 3-epimerase from Clostridium cellulolyticum H10 and its complex with ketohexose sugars. Authors: Chan, H.C. / Zhu, Y. / Hu, Y. / Ko, T.P. / Huang, C.H. / Ren, F. / Chen, C.C. / Ma, Y. / Guo, R.T. / Sun, Y. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.8 KB | Display | ![]() |
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PDB format | ![]() | 205.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vniSC ![]() 3vnjC ![]() 3vnlC ![]() 3vnmC 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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Unit cell |
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Components
#1: Protein | Mass: 33076.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-FUD / #3: Chemical | ChemComp-MN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.2M tri-sodium citrate dehydrate, 17-20% Polyethylene Glycol 3350, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→25 Å / Num. obs: 104455 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rsym value: 0.058 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 10428 / Rsym value: 0.46 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VNI Resolution: 2.02→25 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.02→25 Å
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