+Open data
-Basic information
Entry | Database: PDB / ID: 3uyc | ||||||
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Title | Designed protein KE59 R8_2/7A | ||||||
Components | Kemp eliminase KE59 R8_2/7A | ||||||
Keywords | LYASE / Structural Genomics / Israel Structural Proteomics Center / ISPC / Beta Barrel | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / PHOSPHATE ION Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Khersonsky, O. / Kiss, G. / Roethlisberger, D. / Dym, O. / Albeck, S. / Houk, K.N. / Baker, D. / Tawfik, D.S. / Israel Structural Proteomics Center (ISPC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. Authors: Khersonsky, O. / Kiss, G. / Rothlisberger, D. / Dym, O. / Albeck, S. / 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 | 3uyc.cif.gz | 107.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uyc.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 3uyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/3uyc ftp://data.pdbj.org/pub/pdb/validation_reports/uy/3uyc | HTTPS FTP |
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-Related structure data
Related structure data | 3uxaC 3uxdC 3uy7C 3uy8C 3uz5C 3uzjC 1igsS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 2 - 247 / Label seq-ID: 2 - 247
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-Components
#1: Protein | Mass: 28368.781 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) / References: Lyases #2: Chemical | #3: 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: 2.18 Å3/Da / Density % sol: 43.45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30% PEG2000 MME, 0.1 M potassium thiocyanate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 11, 2009 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→41.595 Å / Num. all: 25786 / Num. obs: 25219 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.063 / Rsym value: 0.111 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 6.4 / Rsym value: 0.427 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IGS Resolution: 2.2→41.595 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.879 / SU B: 7.075 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.255 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 24.541 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→41.595 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1972 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.259 Å / Total num. of bins used: 20
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