+Open data
-Basic information
Entry | Database: PDB / ID: 8uat | ||||||
---|---|---|---|---|---|---|---|
Title | Thermus scotoductus SA-01 Ene-reductase Compound 3b Complex | ||||||
Components | NADPH dehydrogenase | ||||||
Keywords | FLAVOPROTEIN / Oxidoreductase / Complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus scotoductus SA-01 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Wilson, L.A. / Guddat, L.W. / Schenk, G. / Scott, C. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Catalysts / Year: 2024 Title: Structural Characterization of Enzymatic Interactions with Functional Nicotinamide Cofactor Biomimetics Authors: Rocha, R.A. / Wilson, L.A. / Schwartz, B.D. / Warden, A.C. / Guddat, L.W. / Speight, R.E. / Malins, L. / Schenk, G. / Scott, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8uat.cif.gz | 1012.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8uat.ent.gz | 839.8 KB | Display | PDB format |
PDBx/mmJSON format | 8uat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uat_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8uat_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 8uat_validation.xml.gz | 106.8 KB | Display | |
Data in CIF | 8uat_validation.cif.gz | 139.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/8uat ftp://data.pdbj.org/pub/pdb/validation_reports/ua/8uat | HTTPS FTP |
-Related structure data
Related structure data | 8uajC 8uarC 8uasC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 8 molecules BCDEFGHA
#1: Protein | Mass: 40197.223 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus scotoductus SA-01 (bacteria) / Strain: ATCC 700910 / SA-01 / Gene: TSC_p800090 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E8PRF1 |
---|
-Non-polymers , 6 types, 247 molecules
#2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-W3X / Mass: 244.289 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16N2O2 / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.05 % |
---|---|
Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 15% isopropanol, 0.1 M sodium citrate, pH 5, containing 10% w/v PEG10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95374 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→48.75 Å / Num. obs: 86497 / % possible obs: 94.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 50.8 Å2 / CC1/2: 0.956 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.179 / Rrim(I) all: 0.287 / Χ2: 0.4 / Net I/σ(I): 2.8 / Num. measured all: 201370 |
Reflection shell | Resolution: 2.75→2.8 Å / % possible obs: 53.2 % / Redundancy: 2 % / Rmerge(I) obs: 1.234 / Num. measured all: 5252 / Num. unique obs: 2582 / CC1/2: 0.164 / Rpim(I) all: 1.024 / Rrim(I) all: 1.614 / Χ2: 0.23 / Net I/σ(I) obs: 0.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→48.75 Å / SU ML: 0.4836 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.8995 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.76→48.75 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|