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Open data
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Basic information
Entry | Database: PDB / ID: 6fpo | ||||||
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Title | High resolution structure of native Hydrogenase (Hyd-1) | ||||||
![]() | (Hydrogenase-1 ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / NiFe hydrogenase / Iron sulphur cluster / periplasm / hydrogen | ||||||
Function / homology | ![]() hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration ...hydrogen metabolic process / fermentation / hydrogenase (acceptor) / anaerobic electron transport chain / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / periplasmic side of plasma membrane / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / cellular response to starvation / 4 iron, 4 sulfur cluster binding / outer membrane-bounded periplasmic space / electron transfer activity / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carr, S.B. / Armstrong, F.A. / Evans, R.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase. Authors: Evans, R.M. / Ash, P.A. / Beaton, S.E. / Brooke, E.J. / Vincent, K.A. / Carr, S.B. / Armstrong, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 758.5 KB | Display | ![]() |
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PDB format | ![]() | 616 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 884.2 KB | Display | ![]() |
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Full document | ![]() | 890.6 KB | Display | |
Data in XML | ![]() | 79.7 KB | Display | |
Data in CIF | ![]() | 122.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lryC ![]() 6fpiC ![]() 6fpwC ![]() 6g7rC ![]() 6galC ![]() 6gamC ![]() 6ganC ![]() 4uscS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Hydrogenase-1 ... , 2 types, 4 molecules STLM
#1: Protein | Mass: 36814.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 64767.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 1 types, 2 molecules ![](data/chem/img/LMT.gif)
#6: Sugar |
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-Non-polymers , 10 types, 1765 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/SF3.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/LI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/SF3.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FCO.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/LI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-LI / | #12: Chemical | #13: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 46.4 % / Description: Rods with rectangular cross-section |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 100 mM tris pH 8.1 200 mM LiSO4 150 mM NaCl 20-22% PEG 3350 PH range: 8.0-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→99.55 Å / Num. obs: 773665 / % possible obs: 99.8 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 11.3 % / Rmerge(I) obs: 2.21 / Mean I/σ(I) obs: 1.4 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4USC Resolution: 1.05→91.55 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.754 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.021 / 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: 12.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→91.55 Å
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Refine LS restraints |
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