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- PDB-8w0k: Minimal PutA proline dehydrogenase domain (design #2) complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8w0k | ||||||
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Title | Minimal PutA proline dehydrogenase domain (design #2) complexed with 1-hydroxyethane-1-sulfonate | ||||||
![]() | Bifunctional protein PutA fusion protein | ||||||
![]() | OXIDOREDUCTASE / BETA/ALPHA BARREL / FLAVOENZYME / PROLINE CATABOLISM | ||||||
Function / homology | ![]() proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanner, J.J. / Meeks, K.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1) Authors: Meeks, K.R. / Bogner, A.N. / Tanner, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 309.6 KB | Display | ![]() |
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PDB format | ![]() | 247.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Data in CIF | ![]() | 48.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8td2C ![]() 8td3C ![]() 8td4C ![]() 8td5C ![]() 8td6C ![]() 8td7C ![]() 8td8C ![]() 8td9C ![]() 8tdbC ![]() 8tdcC ![]() 8tddC ![]() 8vreC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 43773.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: F7X6I3, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase #2: Chemical | #3: Chemical | Mass: 126.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O4S / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Reservoir contained 0.2 M sodium formate and 20% (w/v) PEG 3350. Enzyme solution contained 20 mM 1-hydroxyethane-1-sulfonate. Crystal was soaked in cryobuffer containing 20% PEG 200 and 20 ...Details: Reservoir contained 0.2 M sodium formate and 20% (w/v) PEG 3350. Enzyme solution contained 20 mM 1-hydroxyethane-1-sulfonate. Crystal was soaked in cryobuffer containing 20% PEG 200 and 20 mM 1-hydroxyethane-1-sulfonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→49.5 Å / Num. obs: 226093 / % possible obs: 88.7 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.026 / Rrim(I) all: 0.05 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.42→1.44 Å / % possible obs: 57.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / Num. measured all: 14268 / Num. unique obs: 3812 / CC1/2: 0.823 / Rpim(I) all: 0.307 / Rrim(I) all: 0.604 / Net I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→49.5 Å
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Refine LS restraints |
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LS refinement shell |
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