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- PDB-6gsd: Plantago Major multifunctional oxidoreductase in complex with pro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gsd | ||||||
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Title | Plantago Major multifunctional oxidoreductase in complex with progesterone and NADP+ | ||||||
![]() | Progesterone 5-beta-reductase | ||||||
![]() | OXIDOREDUCTASE / Progesterone Reductase / Iridoid synthase / SDR / enzyme evolution | ||||||
Function / homology | ![]() 3beta-hydroxy-Delta5-steroid dehydrogenase / cholesterol dehydrogenase activity / 3-beta-hydroxy-delta5-steroid dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-CH group of donors / lipid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fellows, R. / Silva, C. / Russo, C.M. / Lee, S.G. / Jez, J.M. / Chisholm, J.D. / Zubieta, C. / Nanao, M. | ||||||
![]() | ![]() Title: A multisubstrate reductase from Plantago major: structure-function in the short chain reductase superfamily. Authors: Fellows, R. / Russo, C.M. / Silva, C.S. / Lee, S.G. / Jez, J.M. / Chisholm, J.D. / Zubieta, C. / Nanao, M.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.1 KB | Display | ![]() |
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PDB format | ![]() | 129.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mlhC ![]() 5mlmC ![]() 5mlrC ![]() 2v6fS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44113.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: D6N9X1, 3beta-hydroxy-Delta5-steroid dehydrogenase |
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#2: Chemical | ChemComp-STR / |
#3: Chemical | ChemComp-NAD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis Tris Propane, 5% glycerol, and 16.5% to 19% Peg 5K MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 25, 2018 / Details: MIRROR and CRLs |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→68 Å / Num. obs: 13258 / % possible obs: 95 % / Redundancy: 7.6 % / CC1/2: 0.91 / Rrim(I) all: 0.092 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.59→2.65 Å / Mean I/σ(I) obs: 1 / CC1/2: 0.27 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2V6F Resolution: 2.7→39.419 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.33 / Phase error: 28.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→39.419 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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