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Open data
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Basic information
Entry | Database: PDB / ID: 6fpw | ||||||
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Title | Structure of fully reduced Hydrogenase (Hyd-1) | ||||||
![]() | (Hydrogenase-1 ...![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() hydrogen metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lryC ![]() 6fpiC ![]() 6fpoC ![]() 6g7rC ![]() 6galC ![]() 6gamC ![]() 6ganC ![]() 5lmmS 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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Unit cell |
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Components
-Hydrogenase-1 ... , 2 types, 4 molecules STLM
#1: Protein | Mass: 36814.676 Da / Num. of mol.: 2 / Fragment: UNP residues 46-372 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 64751.387 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 , 8 types, 1289 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/SF3.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EJ2.gif)
![](data/chem/img/MG.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/EJ2.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ![]() #5: Chemical | #7: Chemical | ChemComp-CL / ![]() #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-SO4 / | ![]() #11: 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: 296 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 100 mM bis-tris pH 5.7 200 mM LiSO4 150 mM NaCl 19-22% PEG 3350 PH range: 5.5-5.9 / Temp details: Ambient temperature of anaerobic chamber |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.35→97.7 Å / Num. obs: 366570 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5LMM Resolution: 1.35→91.46 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.783 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→91.46 Å
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Refine LS restraints |
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