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Yorodumi- PDB-5wkr: Crystal structure of chalcone isomerase engineered from ancestral... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wkr | ||||||
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Title | Crystal structure of chalcone isomerase engineered from ancestral inference complexed with naringenin (ancCC) | ||||||
Components | Engineered Chalcone Isomerase ancCC | ||||||
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 / NARINGENIN Function and homology information | ||||||
Biological species | unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 5wkr.cif.gz | 274.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wkr.ent.gz | 227 KB | Display | PDB format |
PDBx/mmJSON format | 5wkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wkr_validation.pdf.gz | 765.1 KB | Display | wwPDB validaton report |
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Full document | 5wkr_full_validation.pdf.gz | 769.4 KB | Display | |
Data in XML | 5wkr_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 5wkr_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/5wkr ftp://data.pdbj.org/pub/pdb/validation_reports/wk/5wkr | HTTPS FTP |
-Related structure data
Related structure data | 5wksC 5wl3C 5wl4C 5wl5C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23947.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others) #2: Chemical | ChemComp-NAR / | #3: Chemical | #4: Chemical | #5: 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: 2.6 Å3/Da / Density % sol: 52.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 42%MPD, 50mM acetic acid |
-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: Oct 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→33.52 Å / Num. obs: 98865 / % possible obs: 99.8 % / Redundancy: 6.7 % / Net I/σ(I): 11.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DOI Resolution: 1.4→33.514 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→33.514 Å
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Refine LS restraints |
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LS refinement shell |
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