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Yorodumi- PDB-6c7m: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 19... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c7m | ||||||
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Title | Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 19 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: 1.45 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 | 6c7m.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c7m.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 6c7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c7m_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 6c7m_full_validation.pdf.gz | 443.9 KB | Display | |
Data in XML | 6c7m_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 6c7m_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/6c7m ftp://data.pdbj.org/pub/pdb/validation_reports/c7/6c7m | HTTPS FTP |
-Related structure data
Related structure data | 6c7hC 6c7tC 6c7vC 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: 29328.545 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: Chemical | #3: 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: 3.59 Å3/Da / Density % sol: 65.75 % |
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Crystal grow | Temperature: 277 K / Method: small tubes / pH: 7.25 / 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 3, 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: 1.45→19.69 Å / Num. obs: 76007 / % possible obs: 99.09 % / Redundancy: 2 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01004 / Rrim(I) all: 0.0142 / Net I/σ(I): 30.07 |
Reflection shell | Resolution: 1.45→1.502 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7378 / Mean I/σ(I) obs: 1 / Num. unique obs: 7064 / CC1/2: 0.488 / Rrim(I) all: 1.043 / % possible all: 93.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D30 Resolution: 1.45→19.69 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→19.69 Å
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Refine LS restraints |
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LS refinement shell |
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