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Yorodumi- PDB-7eqk: Structural and mechanistic studies of a novel non-heme iron epime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eqk | |||||||||
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Title | Structural and mechanistic studies of a novel non-heme iron epimerase/lyase and its utilization in chemoselective synthesis. | |||||||||
Components | Cupin domain-containing protein | |||||||||
Keywords | ISOMERASE / non-heme iron epimerase/lyase | |||||||||
Function / homology | RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / 1-(1~{H}-indol-3-yl)ethanone / : / GLYCOLIC ACID / (E)-3-(1H-indol-3-yl)-2-oxidanyl-but-2-enoic acid / Cupin domain-containing protein Function and homology information | |||||||||
Biological species | Streptomyces albus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04001020299 Å | |||||||||
Authors | Li, T.L. / Li, Y.S. / Chen, M.H. | |||||||||
Citation | Journal: Acs Catalysis / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eqk.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eqk.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 7eqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/7eqk ftp://data.pdbj.org/pub/pdb/validation_reports/eq/7eqk | HTTPS FTP |
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-Related structure data
Related structure data | 7eu6C 7eueC 7eupC 7euzC 6j4cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 13831.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces albus (bacteria) / Gene: stnK3, G3260_000576 / Production host: Escherichia coli (E. coli) / References: UniProt: L7PIL3 |
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-Non-polymers , 5 types, 107 molecules
#2: Chemical | #3: Chemical | ChemComp-GOA / | #4: Chemical | ChemComp-5RN / | #5: Chemical | ChemComp-JAX / ( | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.56 % |
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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: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→30 Å / Num. obs: 19749 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 33.5243086976 Å2 / Rsym value: 0.07 / Net I/σ(I): 32.84 |
Reflection shell | Resolution: 2.04→2.11 Å / Rmerge(I) obs: 0.738 / Num. unique obs: 1912 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J4C Resolution: 2.04001020299→28.9588223376 Å / SU ML: 0.25789248673 / Cross valid method: NONE / σ(F): 1.36651513816 / Phase error: 24.8507519835 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: 34.6291999048 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04001020299→28.9588223376 Å
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Refine LS restraints |
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LS refinement shell |
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