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Yorodumi- PDB-7y8m: Structure of ScIRED-R2-V3 from Streptomyces clavuligerus in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y8m | ||||||
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Title | Structure of ScIRED-R2-V3 from Streptomyces clavuligerus in complex with 5-(3-fluorophenyl)-3,4-dihydro-2H-pyrrole | ||||||
Components | reductase | ||||||
Keywords | HYDROLASE/INHIBITOR / substrate binding / HYDROLASE-inhibitor complex | ||||||
Function / homology | Chem-NDP / 2-[2,5-bis(fluoranyl)phenyl]pyrrolidine Function and homology information | ||||||
Biological species | Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 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. #1: 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 | 7y8m.cif.gz | 232.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y8m.ent.gz | 188.3 KB | Display | PDB format |
PDBx/mmJSON format | 7y8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y8m_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 7y8m_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 7y8m_validation.xml.gz | 46.6 KB | Display | |
Data in CIF | 7y8m_validation.cif.gz | 65.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/7y8m ftp://data.pdbj.org/pub/pdb/validation_reports/y8/7y8m | HTTPS FTP |
-Related structure data
Related structure data | 7y8kC 7y8lC 7y8nC 4oqyS 7fel 7fey 7ffb 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO
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-Components
#1: Protein | Mass: 30523.529 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-Q0R / #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: 2.57 Å3/Da / Density % sol: 52.09 % |
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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: 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: 2.28→37.3 Å / Num. obs: 57291 / % possible obs: 99.9 % / Redundancy: 4.94 % / Biso Wilson estimate: 34.91 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.88 |
Reflection shell | Resolution: 2.28→2.38 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.98 / Num. unique obs: 3621 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OQY Resolution: 2.28→34.36 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.41 / 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: 106.55 Å2 / Biso mean: 39.31 Å2 / Biso min: 17.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.28→34.36 Å
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Refine LS restraints NCS |
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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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