+Open data
-Basic information
Entry | Database: PDB / ID: 5fep | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | HydE from T. maritima in complex with (2R,4R)-MeTDA | |||||||||
Components | [FeFe] hydrogenase maturase subunit HydE | |||||||||
Keywords | OXIDOREDUCTASE / Radical SAM enzyme / complex / FeFe-hydrogenase maturase | |||||||||
Function / homology | Function and homology information water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / organonitrogen compound biosynthetic process / 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 / : / organonitrogen compound biosynthetic process / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity / oxidoreductase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | 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 | France, 2items
| |||||||||
Citation | Journal: Nat.Chem. / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fep.cif.gz | 113 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fep.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 5fep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/5fep ftp://data.pdbj.org/pub/pdb/validation_reports/fe/5fep | 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 (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Thermotoga maritima (bacteria) / Gene: TM_1269, THEMA_07990, Tmari_1274 / Production host: Escherichia coli (E. coli) References: UniProt: Q9X0Z6, Oxidoreductases; Acting on a sulfur group of donors |
---|
-Non-polymers , 6 types, 494 molecules
#2: Chemical | ChemComp-SF4 / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#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: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, Lithium sulfate, CHAPS, TrisHCl |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.45→44.02 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|