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Yorodumi- PDB-5d37: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 16... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d37 | ||||||
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Title | Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 16 round 7 | ||||||
Components | De novo kemp eliminase KE07 round 7 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.04 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 16 round 7 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 | 5d37.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d37.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 5d37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/5d37 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/5d37 | HTTPS FTP |
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-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: 29112.182 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) #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: 2.42 Å3/Da / Density % sol: 49.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 11% (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: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→42.83 Å / Num. obs: 36939 / % possible obs: 99.94 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.1246 / Net I/σ(I): 11.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IIV Resolution: 2.04→42.826 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.53 / Phase error: 29.99 / 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: 2.04→42.826 Å
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Refine LS restraints |
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LS refinement shell |
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