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Yorodumi- PDB-6dc1: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 25... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dc1 | ||||||
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Title | Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 25 round 7 | ||||||
Components | Kemp eliminase KE07 | ||||||
Keywords | LYASE / Kemp Eliminase / Directed Evolution / KE07 / DE NOVO PROTEIN | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 5-nitro-2-oxidanyl-benzenecarbonitrile / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Jackson, C.J. / Hong, N.-S. / Carr, P.D. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: The evolution of multiple active site configurations in a designed enzyme. Authors: Hong, N.S. / Petrovic, D. / Lee, R. / Gryn'ova, G. / Purg, M. / Saunders, J. / Bauer, P. / Carr, P.D. / Lin, C.Y. / Mabbitt, P.D. / Zhang, W. / Altamore, T. / Easton, C. / Coote, M.L. / ...Authors: Hong, N.S. / Petrovic, D. / Lee, R. / Gryn'ova, G. / Purg, M. / Saunders, J. / Bauer, P. / Carr, P.D. / Lin, C.Y. / Mabbitt, P.D. / Zhang, W. / Altamore, T. / Easton, C. / Coote, M.L. / Kamerlin, S.C.L. / Jackson, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dc1.cif.gz | 591.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dc1.ent.gz | 488.5 KB | Display | PDB format |
PDBx/mmJSON format | 6dc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dc1_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6dc1_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6dc1_validation.xml.gz | 120.1 KB | Display | |
Data in CIF | 6dc1_validation.cif.gz | 164.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/6dc1 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/6dc1 | HTTPS FTP |
-Related structure data
Related structure data | 6c7hC 6c7mC 6c7tC 6c7vC 6c8bC 6caiC 6ct3C 6dkvC 6dnjC 5d33S 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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Unit cell |
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-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 29183.256 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-Non-polymers , 5 types, 715 molecules
#2: Chemical | ChemComp-6VP / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: 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: 2.62 Å3/Da / Density % sol: 53.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15% PEG3350, 0.1M Bis-trispropane pH 7.5, 0.2M NaF |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2017 |
Radiation | Monochromator: 0.9537 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→47.26 Å / Num. obs: 99503 / % possible obs: 99.7 % / Redundancy: 8.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.177 / Rrim(I) all: 0.189 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.68→2.73 Å / Redundancy: 9.5 % / Rmerge(I) obs: 4.5 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4967 / CC1/2: 0.345 / Rrim(I) all: 4.8 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D33 Resolution: 2.68→47.263 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.57 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→47.263 Å
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Refine LS restraints |
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LS refinement shell |
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