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- PDB-7x7w: The X-ray Crystallographic Structure of D-Psicose 3-epimerase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7x7w | ||||||||||||
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Title | The X-ray Crystallographic Structure of D-Psicose 3-epimerase from Clostridia bacterium | ||||||||||||
![]() | D-PSICOSE 3-EPIMERASE | ||||||||||||
![]() | ISOMERASE / D-Psicose 3-epimerase | ||||||||||||
Function / homology | : ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Li, Z.F. / Ban, X.F. / Xie, X.F. / Tian, Y.X. / Li, C.M. / Gu, Z.B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of a novel homodimeric D-allulose 3-epimerase from a Clostridia bacterium Authors: Xie, X. / Tian, Y. / Ban, X. / Li, C. / Yang, H. / Li, Z. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.8 KB | Display | ![]() |
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PDB format | ![]() | 97.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vnkS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 32348.537 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Succine acid pH 7.0, 0.1 M HEPES pH7.0, 1% w/v PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→37.95 Å / Num. obs: 37135 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 34.68 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 0.124 / Num. unique obs: 2994 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3VNK Resolution: 2.097→37.939 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 34.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96 Å2 / Biso mean: 50.2439 Å2 / Biso min: 27.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.097→37.939 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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