[English] 日本語
Yorodumi- PDB-6sg2: FeFe Hydrogenase from Desulfovibrio desulfuricans in Hinact state -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sg2 | ||||||
---|---|---|---|---|---|---|---|
Title | FeFe Hydrogenase from Desulfovibrio desulfuricans in Hinact state | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE / Hydrogenase / iron-sulfur protein / Hinact / Desulfovibrio desulfuricans | ||||||
Function / homology | Function and homology information ferredoxin hydrogenase activity / iron-sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Galle, L.M. / Span, I. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Caught in the H inact : Crystal Structure and Spectroscopy Reveal a Sulfur Bound to the Active Site of an O 2 -stable State of [FeFe] Hydrogenase. Authors: Rodriguez-Macia, P. / Galle, L.M. / Bjornsson, R. / Lorent, C. / Zebger, I. / Yoda, Y. / Cramer, S.P. / DeBeer, S. / Span, I. / Birrell, J.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6sg2.cif.gz | 199.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6sg2.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6sg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sg2_validation.pdf.gz | 897.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6sg2_full_validation.pdf.gz | 899.5 KB | Display | |
Data in XML | 6sg2_validation.xml.gz | 20 KB | Display | |
Data in CIF | 6sg2_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/6sg2 ftp://data.pdbj.org/pub/pdb/validation_reports/sg/6sg2 | HTTPS FTP |
-Related structure data
Related structure data | 1hfeS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43223.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Gene: hydA, DDE01_08480 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y3TCU2 | ||||||
---|---|---|---|---|---|---|---|
#2: Protein | Mass: 10082.425 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Production host: Escherichia coli (E. coli) | ||||||
#3: Chemical | #4: Chemical | ChemComp-LFH / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.58 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.9 M LiCl, 26% PEG6000, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→43.45 Å / Num. obs: 46365 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 20.41 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 12.5 % / Rmerge(I) obs: 2.11 / Num. unique obs: 2253 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HFE Resolution: 1.65→43.448 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.702 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.106 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.638 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→43.448 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|