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- PDB-8td7: Structure of PYCR1 complexed with 2S-hydroxy-3-methylbutyric acid -
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Open data
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Basic information
Entry | Database: PDB / ID: 8td7 | ||||||
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Title | Structure of PYCR1 complexed with 2S-hydroxy-3-methylbutyric acid | ||||||
![]() | Pyrroline-5-carboxylate reductase 1, mitochondrial | ||||||
![]() | OXIDOREDUCTASE/INHIBITOR / AMINO-ACID BIOSYNTHESIS / OXIDOREDUCTASE / PROLINE BIOSYNTHESIS / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | ![]() pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / proline biosynthetic process / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / cellular response to oxidative stress / mitochondrial matrix / mitochondrion / identical protein 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 | ![]() | 520.4 KB | Display | ![]() |
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PDB format | ![]() | 427.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 55 KB | Display | |
Data in CIF | ![]() | 78.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8td2C ![]() 8td3C ![]() 8td4C ![]() 8td5C ![]() 8td6C ![]() 8td8C ![]() 8td9C ![]() 8tdbC ![]() 8tdcC ![]() 8tddC ![]() 8vreC ![]() 8w0kC 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 33532.574 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P32322, pyrroline-5-carboxylate reductase #2: Chemical | ChemComp-LHV / ( #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PEG / | #5: 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: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Reservoir contained 300 mM Li2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM (S)-(+)-2-hydroxy-3-methylbutyric acid. Crystal was soaked in cryobuffer ...Details: Reservoir contained 300 mM Li2SO4, 19% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 16 mM (S)-(+)-2-hydroxy-3-methylbutyric acid. Crystal was soaked in cryobuffer containing 0 mM Li2SO4, 20% PEG 200, and 125 mM (S)-(+)-2-hydroxy-3-methylbutyric acid |
-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: Feb 18, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→90.76 Å / Num. obs: 205851 / % possible obs: 98.1 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.029 / Rrim(I) all: 0.058 / Net I/σ(I): 13.6 / Num. measured all: 774215 |
Reflection shell | Resolution: 1.61→1.64 Å / % possible obs: 98.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.981 / Num. measured all: 36801 / Num. unique obs: 10228 / CC1/2: 0.595 / Rpim(I) all: 0.586 / Rrim(I) all: 1.147 / Net I/σ(I) obs: 1.3 |
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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: 1.61→90.76 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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