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Yorodumi- PDB-3nq8: Optimization of the in silico designed Kemp eliminase KE70 by com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nq8 | ||||||
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Title | Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R4 8/5A | ||||||
Components | deoxyribose phosphate aldolase | ||||||
Keywords | LYASE / TIM / Structural Genomics / Israel Structural Proteomics Center / ISPC | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / BENZAMIDINE / NITRATE ION Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Khersonsky, O. / Rothlisberge, D. / Wollacott, A.M. / Dym, O. / Baker, D. / Tawfik, D.S. / Israel Structural Proteomics Center (ISPC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution Authors: Khersonsky, O. / Rothlisberger, D. / Wollacott, A.M. / Murphy, P. / Dym, O. / Albeck, S. / Kiss, G. / Houk, K.N. / Baker, D. / Tawfik, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nq8.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nq8.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 3nq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nq8_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 3nq8_full_validation.pdf.gz | 443.9 KB | Display | |
Data in XML | 3nq8_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 3nq8_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/3nq8 ftp://data.pdbj.org/pub/pdb/validation_reports/nq/3nq8 | HTTPS FTP |
-Related structure data
Related structure data | 3npuC 3npvC 3npwC 3npxC 3nq2C 3nqvC 3nr0C 3q2dC 1jcjS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28497.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-BEN / | #4: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE WILD TYPE HAS BEEN ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE WILD TYPE HAS BEEN DEPOSITED TO PDB, 3NPU AND 3NPV. THIS SEQUENCE IS ALA 0, SER 19, GLY 239 INSERTION AND K28N, Y47F, W71C, H165Y, K196N, A203V MUTANT. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.45 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 0.1M Ammonium Nitrat, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å |
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Detector | Detector: CCD / Date: Dec 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 43950 / Num. obs: 43027 / % possible obs: 97.9 % / Redundancy: 20.5 % / Biso Wilson estimate: 14.63 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.053 / Net I/σ(I): 57.28 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 23.1 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 13.6 / Num. unique all: 2163 / Rsym value: 0.211 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JCJ Resolution: 1.4→49.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.549 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.627 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→49.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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