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- PDB-7eup: 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: 7eup | ||||||
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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 / : / (2S,3R)-2-azanyl-3-phenyl-butanoic acid / 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 | ![]() | 71.9 KB | Display | ![]() |
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PDB format | ![]() | 42.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7eqkC ![]() 7eu6C ![]() 7eueC ![]() 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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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 | #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: 2.71 Å3/Da / Density % sol: 54.64 % |
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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: 2.11→30 Å / Num. obs: 17329 / % possible obs: 96.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 31.4590347307 Å2 / Rsym value: 0.046 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.11→2.19 Å / Num. unique obs: 1728 / Rsym value: 0.524 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6J4C Resolution: 2.1104343131→23.1942902442 Å / SU ML: 0.188487912494 / Cross valid method: NONE / σ(F): 1.3677339183 / Phase error: 21.8877147141 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: 32.8330893076 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1104343131→23.1942902442 Å
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Refine LS restraints |
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LS refinement shell |
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