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- PDB-3v9k: Crystal structure of mouse 1-pyrroline-5-carboxylate dehydrogenas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v9k | ||||||
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Title | Crystal structure of mouse 1-pyrroline-5-carboxylate dehydrogenase complexed with the product glutamate | ||||||
![]() | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / aldehyde dehydrogenase / Rossmann fold / nucleotide binding / acting on aldehyde or oxo group of donors / NAD or NADP as acceptor / mitochondria | ||||||
Function / homology | ![]() Proline catabolism / Glyoxylate metabolism and glycine degradation / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / aldehyde dehydrogenase (NAD+) activity / mitochondrial matrix / mitochondrion / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanner, J.J. / Srivastava, D. | ||||||
![]() | ![]() Title: The Three-Dimensional Structural Basis of Type II Hyperprolinemia. Authors: Srivastava, D. / Singh, R.K. / Moxley, M.A. / Henzl, M.T. / Becker, D.F. / 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 | ![]() | 422.3 KB | Display | ![]() |
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PDB format | ![]() | 339.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.9 KB | Display | ![]() |
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Full document | ![]() | 461.1 KB | Display | |
Data in XML | ![]() | 44.9 KB | Display | |
Data in CIF | ![]() | 68.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v9gC ![]() 3v9hC ![]() 3v9iC ![]() 3v9jSC ![]() 3v9lC 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: 61954.215 Da / Num. of mol.: 2 / Fragment: UNP residues 21-562 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: reservoir: 20-25% w/v PEG3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5, cryoprotectant: 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Apr 27, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.501→46.977 Å / Num. all: 168017 / Num. obs: 168017 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rsym value: 0.066 / Net I/σ(I): 25.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3V9J Resolution: 1.501→46.977 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.9229 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.218 Å2 / ksol: 0.387 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.58 Å2 / Biso mean: 11.1311 Å2 / Biso min: 3.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.501→46.977 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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