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Yorodumi- PDB-5d32: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 11... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d32 | ||||||
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Title | Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 11 round 6 | ||||||
Components | De novo kemp eliminase KE07 round 6 | ||||||
Keywords | DE NOVO PROTEIN / LYASE / Kemp Eliminase / Directed Evolution / KE07 | ||||||
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: 2.1 Å | ||||||
Authors | Jackson, C.J. / Hong, N.-S. / Carr, P.D. | ||||||
Citation | Journal: To Be Published Title: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 11 round 6 Authors: Hong, N.-S. / Jackson, C.J. / Carr, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d32.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d32.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 5d32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d32_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
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Full document | 5d32_full_validation.pdf.gz | 436.9 KB | Display | |
Data in XML | 5d32_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 5d32_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/5d32 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/5d32 | HTTPS FTP |
-Related structure data
Related structure data | 3iivS 5d2p 5d2z 5d31 5d34 5d35 5d36 S: Starting model for refinement |
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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: 29197.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: Lyases; Carbon-carbon lyases; Oxo-acid-lyases #2: 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: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 15% (W/V) PEG 3350, 0.1M BIS-TRIS PROPANE, PH 8.5, 0.2M NAF |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→18.96 Å / Num. obs: 32914 / % possible obs: 99.79 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.1694 / Net I/σ(I): 10.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IIV Resolution: 2.1→18.962 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.11 / 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: 2.1→18.962 Å
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Refine LS restraints |
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LS refinement shell |
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