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Yorodumi- PDB-3npx: Optimization of the in silico designed Kemp eliminase KE70 by com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3npx | ||||||
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Title | Optimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution | ||||||
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 Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 | 3npx.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3npx.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 3npx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3npx_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
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Full document | 3npx_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 3npx_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 3npx_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/3npx ftp://data.pdbj.org/pub/pdb/validation_reports/np/3npx | HTTPS FTP |
-Related structure data
Related structure data | 3npuSC 3npvC 3npwC 3nq2C 3nq8C 3nqvC 3nr0C 3q2dC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27979.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) #2: 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 2 INSERTION AND D23G, Y48F, D212E, H251Y MUTANT. | |
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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: 2.51 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M NaCl, 20% PEG 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. all: 53457 / Num. obs: 53243 / % possible obs: 99.6 % / Redundancy: 9.5 % / Biso Wilson estimate: 19.03 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.095 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.9 / Num. unique all: 5234 / Rsym value: 0.29 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NPU Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.196 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R Free: 0.114 / 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: 19.029 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.793→1.84 Å / Total num. of bins used: 20
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