[English] 日本語
Yorodumi- PDB-6nac: Crystal structure of [FeFe]-hydrogenase I (CpI) solved with singl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nac | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of [FeFe]-hydrogenase I (CpI) solved with single pulse free electron laser data | ||||||||||||
Components | Iron hydrogenase 1 | ||||||||||||
Keywords | OXIDOREDUCTASE / [FeFe]-hydrogenase / reactivity of [FeFe]-hydrogenase / Clostridium pasteurianum / iron sulfur clusters / electron-transfer / catalysis | ||||||||||||
Function / homology | Function and homology information ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||||||||
Biological species | Clostridium pasteurianum (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||||||||
Authors | Cohen, A.E. / Davidson, C.M. / Zadvornyy, O.A. / Keable, S.M. / Lyubimov, A.Y. / Song, J. / McPhillips, S.E. / Soltis, S.M. / Peters, J.W. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Tuning Catalytic Bias of Hydrogen Gas Producing Hydrogenases. Authors: Artz, J.H. / Zadvornyy, O.A. / Mulder, D.W. / Keable, S.M. / Cohen, A.E. / Ratzloff, M.W. / Williams, S.G. / Ginovska, B. / Kumar, N. / Song, J. / McPhillips, S.E. / Davidson, C.M. / ...Authors: Artz, J.H. / Zadvornyy, O.A. / Mulder, D.W. / Keable, S.M. / Cohen, A.E. / Ratzloff, M.W. / Williams, S.G. / Ginovska, B. / Kumar, N. / Song, J. / McPhillips, S.E. / Davidson, C.M. / Lyubimov, A.Y. / Pence, N. / Schut, G.J. / Jones, A.K. / Soltis, S.M. / Adams, M.W.W. / Raugei, S. / King, P.W. / Peters, J.W. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6nac.cif.gz | 269.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6nac.ent.gz | 216.2 KB | Display | PDB format |
PDBx/mmJSON format | 6nac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/6nac ftp://data.pdbj.org/pub/pdb/validation_reports/na/6nac | HTTPS FTP |
---|
-Related structure data
Related structure data | 6n59C 6n6pC 3c8yS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63911.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Clostridium pasteurianum (bacteria) / References: UniProt: P29166, ferredoxin hydrogenase |
---|
-Non-polymers , 5 types, 665 molecules
#2: Chemical | ChemComp-402 / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-SF4 / #4: Chemical | ChemComp-FES / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.83 % |
---|---|
Crystal grow | Temperature: 298 K / Method: batch mode / pH: 4.6 Details: 25% PEG 4000, 0.1M Sodium acetate (pH 4.6), 0.1M Sodium sulfate, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.3099 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Oct 31, 2017 |
Radiation | Monochromator: None (SASE pulse) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3099 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→33.1 Å / Num. obs: 90398 / % possible obs: 95.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 8.44 Å2 / Rmerge(I) obs: 0.652 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 4 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7822 / % possible all: 83.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C8Y Resolution: 1.55→33.097 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.98 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→33.097 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|