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- PDB-4xdc: Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xdc | ||||||
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Title | Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor | ||||||
![]() | Iron hydrogenase 1 | ||||||
![]() | OXIDOREDUCTASE / Hydrogenase / H-cluster | ||||||
Function / homology | ![]() ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Esselborn, J. / Hofmann, E. / Kurisu, G. / Happe, T. | ||||||
![]() | ![]() Title: A structural view of synthetic cofactor integration into [FeFe]-hydrogenases. Authors: Esselborn, J. / Muraki, N. / Klein, K. / Engelbrecht, V. / Metzler-Nolte, N. / Apfel, U.P. / Hofmann, E. / Kurisu, G. / Happe, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 463.2 KB | Display | ![]() |
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PDB format | ![]() | 379.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 53.1 KB | Display | |
Data in CIF | ![]() | 81.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xddC ![]() 5byqC ![]() 5byrC ![]() 5bysC ![]() 3c8yS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 65111.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1244 molecules ![](data/chem/img/402.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 / Details: PEG3000, MgCl / PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92044 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→48.37 Å / Num. obs: 170277 / % possible obs: 99.9 % / Redundancy: 21.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.63→1.67 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 2.21 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3C8Y Resolution: 1.63→47.445 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→47.445 Å
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Refine LS restraints |
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LS refinement shell |
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