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Yorodumi- PDB-7f6x: Structural and mechanistic studies of a novel non-heme iron epime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f6x | |||||||||
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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 / metal ion binding / : / GLYCOLIC ACID / 1H-INDOLE-3-CARBALDEHYDE / Cupin domain-containing protein Function and homology information | |||||||||
Biological species | Streptomyces albus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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-MediatedLewis-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 | 7f6x.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f6x.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 7f6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f6x_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7f6x_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7f6x_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 7f6x_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/7f6x ftp://data.pdbj.org/pub/pdb/validation_reports/f6/7f6x | HTTPS FTP |
-Related structure data
Related structure data | 6j4cS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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.) Streptomyces albus (bacteria) / Gene: stnK3 / Production host: Escherichia coli (E. coli) / References: UniProt: L7PIL3 #2: Chemical | ChemComp-I3A / | #3: Chemical | #4: Chemical | ChemComp-GOA / | #5: Water | ChemComp-HOH / | 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: 2.73 Å3/Da / Density % sol: 55.01 % |
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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: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 23, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.16→30 Å / Num. obs: 16817 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.021 / Rrim(I) all: 0.061 / Χ2: 0.914 / Net I/σ(I): 37.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J4C Resolution: 2.16→28.14 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.195 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.83 Å2 / Biso mean: 25.971 Å2 / Biso min: 9.82 Å2
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Refinement step | Cycle: final / Resolution: 2.16→28.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.162→2.218 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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