+Open data
-Basic information
Entry | Database: PDB / ID: 3uxd | ||||||
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Title | Designed protein KE59 R1 7/10H with dichlorobenzotriazole (DBT) | ||||||
Components | Kemp eliminase KE59 R1 7/10H | ||||||
Keywords | LYASE/LYASE INHIBITOR / Structural Genomics / Israel Structural Proteomics Center / ISPC / Beta Barrel / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 5,7-dichloro-1H-benzotriazole / PHOSPHATE ION Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 3uxd.cif.gz | 209.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uxd.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 3uxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uxd_validation.pdf.gz | 461.2 KB | Display | wwPDB validaton report |
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Full document | 3uxd_full_validation.pdf.gz | 467.1 KB | Display | |
Data in XML | 3uxd_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 3uxd_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/3uxd ftp://data.pdbj.org/pub/pdb/validation_reports/ux/3uxd | HTTPS FTP |
-Related structure data
Related structure data | 3uxaC 3uy7C 3uy8C 3uycSC 3uz5C 3uzjC 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
#1: Protein | Mass: 28749.346 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: Chemical | ChemComp-PO4 / #4: 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: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Wizard screen 1 #30: 1.26 M ammonium sulfate, 0.1 M sodium acetate, pH 4.5, 0.2 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2011 |
Radiation | Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.076 Å / Num. all: 48070 / Num. obs: 47974 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.082 / Rsym value: 0.088 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.221 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3UYC Resolution: 1.8→40.076 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.615 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.156 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40.076 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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