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Yorodumi- PDB-7y8o: Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y8o | ||||||
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Title | Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in complex with 5-(3-fluorophenyl)-3,4-dihydro-2H-pyrrole | ||||||
Components | SciR | ||||||
Keywords | HYDROLASE/INHIBITOR / substrate binding / HYDROLASE-inhibitor complex | ||||||
Function / homology | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2-[2,5-bis(fluoranyl)phenyl]pyrrolidine Function and homology information | ||||||
Biological species | Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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: to be published Title: Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in complex with 5-(3-fluorophenyl)-3,4-dihydro-2H-pyrrole Authors: Zhang, L.L. / Liu, W.D. / Shi, M. / Huang, J.W. / Yang, Y. / Chen, C.C. / Guo, R.T. #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 | 7y8o.cif.gz | 125.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y8o.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 7y8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y8o_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7y8o_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7y8o_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 7y8o_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/7y8o ftp://data.pdbj.org/pub/pdb/validation_reports/y8/7y8o | HTTPS FTP |
-Related structure data
Related structure data | 4oqyS S: Starting model for refinement |
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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) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21(DE3) #2: Chemical | #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: 2.11 Å3/Da / Density % sol: 41.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15% Polyethylene glycol 6000, 0.1 M 2-(4-Morpholino) ethanesulfonic acid pH 6.5, 5% 2-methyl-1,3-propanediol |
-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 5, 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: 2.3→34.7 Å / Num. obs: 43563 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 2186 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OQY Resolution: 2.3→34.58 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.43 / 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: 98.07 Å2 / Biso mean: 27.98 Å2 / Biso min: 13.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→34.58 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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