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Yorodumi- PDB-5d30: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 9 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d30 | ||||||
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Title | Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 9 Round 5 | ||||||
Components | De novo kemp eliminase KE07 round 5 | ||||||
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: 1.69 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 9 Round 5 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 | 5d30.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d30.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 5d30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d30_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 5d30_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 5d30_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 5d30_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/5d30 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/5d30 | HTTPS FTP |
-Related structure data
Related structure data | 2rkxS 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: 29328.545 Da / Num. of mol.: 1 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) |
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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: 3.79 Å3/Da / Density % sol: 67.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 25mM HEPES, pH 7.25, 0.1M NaCl |
-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 23, 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: 1.69→41.92 Å / Num. obs: 48768 / % possible obs: 99.99 % / Redundancy: 19.5 % / Rmerge(I) obs: 0.1255 / Net I/σ(I): 17.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RKX Resolution: 1.69→41.916 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.79 / 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: 1.69→41.916 Å
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Refine LS restraints |
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LS refinement shell |
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