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- PDB-6gm2: [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282D -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gm2 | ||||||
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Title | [FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282D | ||||||
![]() | Iron hydrogenase 1 | ||||||
![]() | OXIDOREDUCTASE / Hydrogenase / H-cluster / semisynthetic enzyme | ||||||
Function / homology | ![]() ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Duan, J. / Esselborn, J. / Hofmann, E. / Winkler, M. / Happe, T. | ||||||
![]() | ![]() Title: Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases. Authors: Duan, J. / Senger, M. / Esselborn, J. / Engelbrecht, V. / Wittkamp, F. / Apfel, U.P. / Hofmann, E. / Stripp, S.T. / Happe, T. / Winkler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.7 KB | Display | ![]() |
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PDB format | ![]() | 188.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 41.1 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6glyC ![]() 6glzC ![]() 6gm0C ![]() 6gm1C ![]() 6gm3C ![]() 6gm4C ![]() 6gm5C ![]() 6gm6C ![]() 6gm7C ![]() 6gm8C ![]() 4xdcS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 65097.379 Da / Num. of mol.: 2 / Mutation: E282D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 89 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: 2.6 Å3/Da / Density % sol: 52.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 21% PEG 4000, 0.4 M MgCl2,0.1 M MES, 19 % glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97863 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.76→47.88 Å / Num. obs: 34211 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 2.58 % / Biso Wilson estimate: 35.32 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.199 / Rrim(I) all: 0.222 / Χ2: 0.895 / Net I/σ(I): 8.03 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XDC Resolution: 2.76→47.88 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.09 Å2 / Biso mean: 34.5591 Å2 / Biso min: 13.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.76→47.88 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %
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