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Yorodumi- PDB-7y8n: Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y8n | ||||||
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Title | Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in complex with 5-(2,5-difluorophenyl)-3,4-dihydro-2H-pyrrole | ||||||
Components | Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / substrate binding / OXIDOREDUCTASE-inhibitor complex | ||||||
Function / homology | Chem-4IS / Chem-NDP Function and homology information | ||||||
Biological species | Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 7y8n.cif.gz | 129.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y8n.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 7y8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/7y8n ftp://data.pdbj.org/pub/pdb/validation_reports/y8/7y8n | HTTPS FTP |
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-Related structure data
Related structure data | 7y8kC 7y8lC 7y8mC 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
#1: Protein | Mass: 30417.490 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: pET32Xa/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Chemical | #3: Chemical | ChemComp-4IS / | #4: 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: 2.06 Å3/Da / Density % sol: 40.29 % 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: 4.6 Details: Ammonium Acetate,Sodium Acetate trihydrate,Polyethylene Glycol 4000, Glycerol |
-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: Jul 8, 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: 2.2→37.13 Å / Num. obs: 49197 / % possible obs: 99.7 % / Redundancy: 4.85 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.038 / Rrim(I) all: 0.085 / Net I/σ(I): 13.18 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.204 / Num. unique obs: 3164 / CC1/2: 0.969 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OQY Resolution: 2.2→37.13 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.52 / 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: 98.81 Å2 / Biso mean: 23.8135 Å2 / Biso min: 9.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→37.13 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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