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- PDB-8td3: Structure of PYCR1 complexed with NADH and (S)-Tetrahydro-2H-pyra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8td3 | ||||||
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Title | Structure of PYCR1 complexed with NADH and (S)-Tetrahydro-2H-pyran-2-carboxylic 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 | ![]() | 529.1 KB | Display | ![]() |
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PDB format | ![]() | 435.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.3 MB | Display | |
Data in XML | ![]() | 58.2 KB | Display | |
Data in CIF | ![]() | 81.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8td2C ![]() 8td4C ![]() 8td5C ![]() 8td6C ![]() 8td7C ![]() 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
-Protein , 1 types, 5 molecules ABCDE
#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 |
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-Non-polymers , 5 types, 817 molecules ![](data/chem/img/NAI.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAI / #3: Chemical | ChemComp-GJM / ( Mass: 130.142 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Reservoir contained 360 mM Li2SO4, 18% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 16 mM Tetrahydropyran-2-carboxylic acid. Crystal was soaked in ...Details: Reservoir contained 360 mM Li2SO4, 18% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 2 mM NADH and 16 mM Tetrahydropyran-2-carboxylic acid. Crystal was soaked in cryobuffer containing 20% PEG 200 and 25 mM Tetrahydropyran-2-carboxylic 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: 1.67→91.86 Å / Num. obs: 187638 / % possible obs: 98.3 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Rrim(I) all: 0.077 / Net I/σ(I): 12.3 / Num. measured all: 851107 |
Reflection shell | Resolution: 1.67→1.7 Å / % possible obs: 97.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 1.066 / Num. measured all: 40878 / Num. unique obs: 9185 / CC1/2: 0.531 / Rpim(I) all: 0.557 / Rrim(I) all: 1.206 / Net I/σ(I) obs: 1.1 |
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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: 1.67→91.86 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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