[English] 日本語
Yorodumi- PDB-6s0g: Crystal structure of ene-reductase GsOYE from Galdieria sulphuraria -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s0g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ene-reductase GsOYE from Galdieria sulphuraria | ||||||
Components | NADPH2 dehydrogenase-like protein | ||||||
Keywords | FLAVOPROTEIN / ene-reductase / Old Yellow Enzyme / Biocatalysis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Galdieria sulphuraria (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Robescu, M.R. / Niero, M. / Hall, M. / Bergantino, E. / Cendron, L. | ||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2020 Title: Two new ene-reductases from photosynthetic extremophiles enlarge the panel of old yellow enzymes: CtOYE and GsOYE. Authors: Robescu, M.S. / Niero, M. / Hall, M. / Cendron, L. / Bergantino, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6s0g.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6s0g.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 6s0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s0g_validation.pdf.gz | 786 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6s0g_full_validation.pdf.gz | 788.1 KB | Display | |
Data in XML | 6s0g_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 6s0g_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/6s0g ftp://data.pdbj.org/pub/pdb/validation_reports/s0/6s0g | HTTPS FTP |
-Related structure data
Related structure data | 6s23C 6s31C 6s32C 1gwjS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45494.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: Gasu_54250 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M2XAQ9 |
---|---|
#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-FMN / |
#4: Chemical | ChemComp-CL / |
#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: 2.12 Å3/Da / Density % sol: 41.92 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M MgCl2 hexahydrate or 0.2 M CaCl2 dihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.0725 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0725 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→45.61 Å / Num. obs: 880814 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 45283 / CC1/2: 0.993 / Rpim(I) all: 0.26 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GWJ Resolution: 1.45→45.61 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 18.49
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→45.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|