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Yorodumi- PDB-5wl5: Crystal structure of chalcone isomerase engineered from ancestral... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wl5 | ||||||
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Title | Crystal structure of chalcone isomerase engineered from ancestral inference (ancR5) | ||||||
Components | Engineered Chalcone Isomerase ancR5 | ||||||
Keywords | ISOMERASE / chalcone isomerase / naringenin / flavanone | ||||||
Function / homology | 10k-s Protein, Hypothetical Protein A; Chain A - #20 / Chalcone isomerase - #10 / Chalcone isomerase / 10k-s Protein, Hypothetical Protein A; Chain A / 3-Layer(bba) Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Function and homology information | ||||||
Biological species | unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.513 Å | ||||||
Authors | Burke, J.R. / Kaltenbach, M. / Tawfik, D.S. / Noel, J.P. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2018 Title: Evolution of chalcone isomerase from a noncatalytic ancestor. Authors: Kaltenbach, M. / Burke, J.R. / Dindo, M. / Pabis, A. / Munsberg, F.S. / Rabin, A. / Kamerlin, S.C.L. / Noel, J.P. / Tawfik, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wl5.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wl5.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 5wl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/5wl5 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/5wl5 | HTTPS FTP |
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-Related structure data
Related structure data | 5wkrC 5wksC 5wl3C 5wl4C 5wl6C 5wl7C 5wl8C 4doiS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23899.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli K-12 (bacteria) | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 3.5mM ammonium sulfate and 100mM TAPS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→57.19 Å / Num. obs: 40583 / % possible obs: 100 % / Redundancy: 16.3 % / Net I/σ(I): 18.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB:4DOI Resolution: 1.513→57.188 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.513→57.188 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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