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Open data
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Basic information
Entry | Database: PDB / ID: 5ff3 | |||||||||
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Title | HydE from T. maritima in complex with 4R-TCA | |||||||||
![]() | [FeFe] hydrogenase maturase subunit HydE | |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | ![]() water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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. | |||||||||
![]() | ![]() 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 | ![]() | 200.2 KB | Display | ![]() |
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PDB format | ![]() | 157 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5fepC ![]() 5fesC ![]() 5fewC ![]() 5fexC ![]() 5fezC ![]() 5ff0C ![]() 5ff2C ![]() 5ff4C ![]() 3ciwS 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
-Protein , 1 types, 1 molecules A
#1: Protein | [ Mass: 39873.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1269, THEMA_07990, Tmari_1274 / Production host: ![]() ![]() ![]() References: UniProt: Q9X0Z6, ![]() |
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-Non-polymers , 8 types, 458 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/CPS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/PRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CPS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/PRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / ![]() | ||||||||||||
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#3: Chemical | ChemComp-CPS / ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-FES / | ![]() #6: Chemical | ChemComp-SAH / | ![]() #7: Chemical | ![]() #8: Chemical | ChemComp-PRS / | #9: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG4000, 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: Jul 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.18→44 Å / Num. obs: 114847 / % possible obs: 99.6 % / Redundancy: 4.5 % / Rsym value: 0.067 / Net I/σ(I): 12.65 |
Reflection shell | Resolution: 1.18→1.25 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.79 / CC1/2: 0.7 / Rsym value: 0.779 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3CIW Resolution: 1.18→43.9 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.182 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.04 Å2
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Refinement step | Cycle: 1 / Resolution: 1.18→43.9 Å
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Refine LS restraints |
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