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- PDB-5ira: Expanding Nature's Catalytic Repertoire -Directed Evolution of an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ira | ||||||
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Title | Expanding Nature's Catalytic Repertoire -Directed Evolution of an Artificial Metalloenzyme for In Vivo Metathesis | ||||||
![]() | Artificial Metathesase | ||||||
![]() | biotin-binding protein / beta barrel / metathesis / organometallic complex | ||||||
Function / homology | Avidin-like / Lipocalin / Beta Barrel / Mainly Beta / Chem-9RU![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heinisch, T. / Jeschek, M. / Reuter, R. / Trindler, C. / Panke, S. / Ward, T.R. | ||||||
![]() | ![]() Title: Directed evolution of artificial metalloenzymes for in vivo metathesis. Authors: Jeschek, M. / Reuter, R. / Heinisch, T. / Trindler, C. / Klehr, J. / Panke, S. / Ward, T.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.5 KB | Display | ![]() |
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PDB format | ![]() | 49.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 927.4 KB | Display | ![]() |
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Full document | ![]() | 934.5 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5f2bC ![]() 2qcbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 16570.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-9RU / [ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 1.5 M AmSO4, 0.1 M Na acetate, pH4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999989 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45.85 Å / Num. obs: 25264 / % possible obs: 100 % / Redundancy: 21.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 19.1 % / Rmerge(I) obs: 1.228 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QCB Resolution: 1.5→45.85 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.995 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→45.85 Å
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Refine LS restraints |
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