+Open data
-Basic information
Entry | Database: PDB / ID: 7y8k | ||||||
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Title | Structure of ScIRED wild-type from Streptomyces clavuligerus | ||||||
Components | Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase | ||||||
Keywords | HYDROLASE / substrate binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Zhang, L.L. / Liu, W.D. / Shi, M. / Huang, J.W. / Yang, Y. / Chen, C.C. / Guo, R.T. | ||||||
Funding support | 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Engineered Imine Reductase for Larotrectinib Intermediate Manufacture Authors: Chen, Q. / Li, B.B. / Zhang, L. / Chen, X.R. / Zhu, X.X. / Chen, F.F. / Shi, M. / Chen, C.C. / Yang, Y. / Guo, R.T. / Liu, W. / Xu, J.H. / Zheng, G.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y8k.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y8k.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 7y8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y8k_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 7y8k_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 7y8k_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 7y8k_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/7y8k ftp://data.pdbj.org/pub/pdb/validation_reports/y8/7y8k | HTTPS FTP |
-Related structure data
Related structure data | 7y8lC 7y8mC 7y8nC 4oqyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 30468.557 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: SCLAV_2776 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E2PUR9 #2: Water | ChemComp-HOH / | |
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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: 2.05 Å3/Da / Density % sol: 40.11 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12% Polyethylene glycol 8000, 0.1 M 2-(4-Morpholino) ethanesulfonic acid pH 6.0, 0.1M Calcium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Jun 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→38.44 Å / Num. obs: 57293 / % possible obs: 99.7 % / Redundancy: 7.69 % / Biso Wilson estimate: 23.28 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.25 |
Reflection shell | Resolution: 2.08→2.18 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 2112 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OQY Resolution: 2.08→38.44 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.3 / 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: 74.55 Å2 / Biso mean: 28.45 Å2 / Biso min: 9.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→38.44 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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