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- PDB-8p5y: Artificial transfer hydrogenase with a Mn-12 cofactor and Strepta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p5y | ||||||
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Title | Artificial transfer hydrogenase with a Mn-12 cofactor and Streptavidin S112Y-K121M mutant | ||||||
![]() | Streptavidin | ||||||
![]() | METAL BINDING PROTEIN / Artificial meatlloenzyme / Transfer hydrogenase / Manganese | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lau, K. / Wang, W. / Pojer, F. / Larabi, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Manganese Transfer Hydrogenases Based on the Biotin-Streptavidin Technology. Authors: Wang, W. / Tachibana, R. / Zou, Z. / Chen, D. / Zhang, X. / Lau, K. / Pojer, F. / Ward, T.R. / Hu, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 294.8 KB | Display | ![]() |
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PDB format | ![]() | 233.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8p5zC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 16647.145 Da / Num. of mol.: 4 / Mutation: S112Y-K121M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 107 molecules ![](data/chem/img/WZQ.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-WZQ / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-BR / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.63 Å3/Da / Density % sol: 24.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Sodium/potassium phosphate, 0.1 M HEPES pH 7.5, 15 % v/v PEG, Smear High, 10 % v/v Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→45.89 Å / Num. obs: 33538 / % possible obs: 95.56 % / Redundancy: 5.2 % / Biso Wilson estimate: 36.65 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1573 / Net I/σ(I): 6.49 |
Reflection shell | Resolution: 1.88→1.94 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 0.75 / Num. unique obs: 2320 / CC1/2: 0.386 / CC star: 0.747 / % possible all: 80.7 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→45.89 Å
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Refine LS restraints |
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LS refinement shell |
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