+Open data
-Basic information
Entry | Database: PDB / ID: 5ff2 | ||||||
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Title | HydE from T. maritima in complex with (2R,4R)-TDA | ||||||
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: 1.47 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. | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ff2.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ff2.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ff2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/5ff2 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/5ff2 | HTTPS FTP |
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-Related structure data
Related structure data | 5fepC 5fesC 5fewC 5fexC 5fezC 5ff0C 5ff3C 5ff4C 3iixS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 39857.277 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 |
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-Non-polymers , 7 types, 458 molecules
#2: Chemical | ChemComp-SF4 / | ||||||||||
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#3: Chemical | ChemComp-CPS / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SAH / | #6: Chemical | ChemComp-5XB / ( | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.79 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å |
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: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→44 Å / Num. obs: 59781 / % possible obs: 98.4 % / Redundancy: 2.9 % / Net I/σ(I): 8.05 |
Reflection shell | Resolution: 1.47→1.56 Å / Rsym value: 0.683 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IIX Resolution: 1.47→38.47 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.473 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.07 / 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: 18.886 Å2
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Refinement step | Cycle: 1 / Resolution: 1.47→38.47 Å
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Refine LS restraints |
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