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Open data
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Basic information
Entry | Database: PDB / ID: 1uc5 | |||||||||
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Title | Structure of diol dehydratase complexed with (R)-1,2-propanediol | |||||||||
![]() | (diol dehydrase ...) x 3 | |||||||||
![]() | LYASE / ALPHA/BETA BARREL | |||||||||
Function / homology | ![]() propanediol dehydratase / propanediol dehydratase activity / cobalamin binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shibata, N. / Nakanishi, Y. / Fukuoka, M. / Yamanishi, M. / Yasuoka, N. / Toraya, T. | |||||||||
![]() | ![]() Title: Structural rationalization for the lack of stereospecificity in coenzyme B12-dependent diol dehydratase Authors: Shibata, N. / Nakanishi, Y. / Fukuoka, M. / Yamanishi, M. / Yasuoka, N. / Toraya, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 364.2 KB | Display | ![]() |
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PDB format | ![]() | 290.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1uc4C ![]() 1egmS 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
-Diol dehydrase ... , 3 types, 6 molecules ALBEGM
#1: Protein | Mass: 60408.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 24141.678 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 19198.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 734 molecules ![](data/chem/img/K.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/PGR.gif)
![](data/chem/img/CNC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/PGR.gif)
![](data/chem/img/CNC.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-NH4 / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 47.85 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / pH: 8 Details: PEG6000, ammonium sulfate, Tris, (R)-1,2,-propanediol, pH 8.0, VAPOR DIFFUSION, temperature 278K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: sandwich-drop vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.708 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / % possible obs: 93.1 % / Observed criterion σ(I): -1 / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.413 / % possible all: 80.8 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. obs: 79408 / Num. measured all: 1033483 |
Reflection shell | *PLUS % possible obs: 80.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EGM Resolution: 2.3→46.85 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→46.85 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Lowest resolution: 30 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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