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Yorodumi- PDB-6c7v: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 22... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c7v | ||||||
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Title | Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 22 round 5 | ||||||
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 Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 | 6c7v.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c7v.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 6c7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/6c7v ftp://data.pdbj.org/pub/pdb/validation_reports/c7/6c7v | HTTPS FTP |
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-Related structure data
Related structure data | 6c7hC 6c7mC 6c7tC 6c8bC 6caiC 6ct3C 6dc1C 6dkvC 6dnjC 5d30S 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
#1: Protein | Mass: 27943.068 Da / Num. of mol.: 1 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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#2: 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: 3.87 Å3/Da / Density % sol: 68.18 % |
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Crystal grow | Temperature: 277 K / Method: slow cooling / Details: 25 mM HEPES pH 7.25, 100 mM NaCl |
-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 | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→19.72 Å / Num. obs: 54654 / % possible obs: 99.89 % / Redundancy: 2 % / Biso Wilson estimate: 28.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0244 / Rrim(I) all: 0.03454 / Net I/σ(I): 10.11 |
Reflection shell | Resolution: 1.64→1.699 Å / Redundancy: 2 % / Rmerge(I) obs: 1.093 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 5353 / CC1/2: 0.309 / Rrim(I) all: 1.546 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D30 Resolution: 1.64→19.72 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→19.72 Å
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Refine LS restraints |
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LS refinement shell |
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