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Open data
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Basic information
Entry | Database: PDB / ID: 5fep | |||||||||
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Title | HydE from T. maritima in complex with (2R,4R)-MeTDA | |||||||||
![]() | [FeFe] hydrogenase maturase subunit HydE | |||||||||
![]() | OXIDOREDUCTASE / Radical SAM enzyme / complex / FeFe-hydrogenase maturase | |||||||||
Function / homology | ![]() water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / : / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity ...water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / : / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity / oxidoreductase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rohac, R. / Amara, P. / Benjdia, A. / Martin, L. / Ruffie, P. / Favier, A. / Berteau, O. / Mouesca, J.M. / Fontecilla-Camps, J.C. / Nicolet, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE. Authors: Rohac, R. / Amara, P. / Benjdia, A. / Martin, L. / Ruffie, P. / Favier, A. / Berteau, O. / Mouesca, J.M. / Fontecilla-Camps, J.C. / Nicolet, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113 KB | Display | ![]() |
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PDB format | ![]() | 83 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 36.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fesC ![]() 5fewC ![]() 5fexC ![]() 5fezC ![]() 5ff0C ![]() 5ff2C ![]() 5ff3C ![]() 5ff4C ![]() 3iixS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | [ Mass: 41025.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9X0Z6, Oxidoreductases; Acting on a sulfur group of donors |
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-Non-polymers , 6 types, 494 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/CPS.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/41K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CPS.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/41K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / | ||||||||
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#3: Chemical | ChemComp-CPS / #4: Chemical | ChemComp-SAM / | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-41K / ( | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, Lithium sulfate, CHAPS, TrisHCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→44.05 Å / Num. obs: 63460 / % possible obs: 99.5 % / Redundancy: 3.4 % / Net I/σ(I): 14.86 |
Reflection shell | Resolution: 1.45→1.54 Å / Rsym value: 0.81 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IIX Resolution: 1.45→44.02 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.394 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069 / 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: 21.714 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→44.02 Å
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Refine LS restraints |
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