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- PDB-5f2b: 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: 5f2b | ||||||
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Title | Expanding Nature's Catalytic Repertoire -Directed Evolution of an Artificial Metalloenzyme for In Vivo Metathesis | ||||||
![]() | Streptavidin | ||||||
![]() | biotin-binding protein / beta barrel / metathesis / organometallic complex | ||||||
Function / homology | ![]() | ||||||
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 | ![]() | 69.9 KB | Display | ![]() |
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PDB format | ![]() | 50.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 915.6 KB | Display | ![]() |
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Full document | ![]() | 925.6 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5iraC ![]() 2qcbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 16598.053 Da / Num. of mol.: 1 / Mutation: V47A,N49K,T114Q,A119G,K121R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-9RU / [ |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1.5 M ammonium sulfate, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.7→54.553 Å / Num. obs: 16547 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Net I/σ(I): 12.6 / Num. measured all: 208507 / Scaling rejects: 5 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QCB Resolution: 1.7→54.55 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2017 / WRfactor Rwork: 0.1378 / FOM work R set: 0.7593 / SU B: 5.793 / SU ML: 0.078 / SU R Cruickshank DPI: 0.098 / SU Rfree: 0.0905 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.091 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 168.39 Å2 / Biso mean: 37.888 Å2 / Biso min: 19.43 Å2
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Refinement step | Cycle: final / Resolution: 1.7→54.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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