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- PDB-7eu6: Structural and mechanistic studies of a novel non-heme iron epime... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7eu6 | ||||||
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Title | Structural and mechanistic studies of a novel non-heme iron epimerase/lyase and its utilization in chemoselective synthesis. | ||||||
![]() | Cupin domain-containing protein | ||||||
![]() | ISOMERASE / non-heme iron epimerase/lyase | ||||||
Function / homology | RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / : / PHOSPHITE ION / Cupin domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, T.L. / Li, Y.S. / Chen, M.H. | ||||||
![]() | ![]() Title: Structural and Mechanistic Bases for StnK3 and Its Mutant-Mediated Lewis-Acid-Dependent Epimerization and Retro-Aldol Reactions. Authors: Chen, M.H. / Li, Y.S. / Hsu, N.S. / Lin, K.H. / Wang, Y.L. / Wang, Z.C. / Chang, C.F. / Lin, J.P. / Chang, C.Y. / Li, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.2 KB | Display | ![]() |
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PDB format | ![]() | 42.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7eqkC ![]() 7eueC ![]() 7eupC ![]() 7euzC ![]() 6j4cS 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / End auth comp-ID: VAL / End label comp-ID: VAL
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Components
#1: Protein | Mass: 13831.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PO3 / | #3: Chemical | #4: 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: 2.75 Å3/Da / Density % sol: 55.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.2 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic, pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 19687 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 29.1066472483 Å2 / Rsym value: 0.052 / Net I/σ(I): 21.15 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.708 / Num. unique obs: 1913 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6J4C Resolution: 2.05010806519→26.1541485906 Å / SU ML: 0.247947966559 / Cross valid method: NONE / σ(F): 1.34434588892 / Phase error: 22.7243337717 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 31.0813185145 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05010806519→26.1541485906 Å
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Refine LS restraints |
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LS refinement shell |
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