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Open data
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Basic information
Entry | Database: PDB / ID: 7e9w | ||||||
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Title | The Crystal Structure of D-psicose-3-epimerase from Biortus. | ||||||
![]() | D-psicose 3-epimerase | ||||||
![]() | ISOMERASE / ion binding / cation binding / metal ion binding | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Wang, F. / Xu, C. / Qi, J. / Zhang, M. / Tian, F. / Wang, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Crystal Structure of D-psicose-3-epimerase from Biortus. Authors: Wang, F. / Xu, C. / Qi, J. / Zhang, M. / Tian, F. / Wang, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 259.4 KB | Display | ![]() |
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PDB format | ![]() | 199 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.4 KB | Display | ![]() |
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Full document | ![]() | 484.7 KB | Display | |
Data in XML | ![]() | 47.5 KB | Display | |
Data in CIF | ![]() | 67.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vniS S: Starting model for refinement |
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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: 35942.328 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 35319 / DSM 5812 / JCM 6584 / H10 / Gene: Ccel_0941 / Production host: ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.02M MgCl2, 0.1M HEPES pH7.5, 22% Polyacrylic acid sodium salt 5,100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5215 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.607 Å / Num. obs: 91449 / % possible obs: 98 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 4468 / CC1/2: 0.829 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3vni Resolution: 2.1→48.607 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.174 / SU B: 4.045 / SU ML: 0.104 / Average fsc free: 0.9328 / Average fsc work: 0.9416 / Cross valid method: FREE R-VALUE / ESU R: 0.17 / ESU R Free: 0.149 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.161 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→48.607 Å
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Refine LS restraints |
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LS refinement shell |
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