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- PDB-4idm: Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4idm | ||||||
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Title | Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis | ||||||
![]() | Delta-1-pyrroline-5-carboxylate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / pyrroline dehydrogenase / Aldehyde dehydrogenase / pyrroline-5-carboxylate dehydrogeanse / pyrroline-5-carboxylic acid / dehydrogenation | ||||||
Function / homology | ![]() L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / cytoplasmic side of plasma membrane / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lagautriere, T. / Bashiri, G. / Baker, E.N. | ||||||
![]() | ![]() Title: Characterization of the proline-utilization pathway in Mycobacterium tuberculosis through structural and functional studies. Authors: Lagautriere, T. / Bashiri, G. / Paterson, N.G. / Berney, M. / Cook, G.M. / Baker, E.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115 KB | Display | ![]() |
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PDB format | ![]() | 93.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 61556.621 Da / Num. of mol.: 1 / Mutation: G505D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: I6X0K4, UniProt: O50443*PLUS, EC: 1.5.1.12 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 0.1 M Bicine/Tris pH 8.1, 12% polyethylene glycol (PEG) 1000, 12% PEG 3350, 12% 2-methyl-2,4-pentandiol (MPD), 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate and 0.03 M ammonium ...Details: 0.1 M Bicine/Tris pH 8.1, 12% polyethylene glycol (PEG) 1000, 12% PEG 3350, 12% 2-methyl-2,4-pentandiol (MPD), 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate and 0.03 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2011 | ||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→39.78 Å / Num. all: 26403 / Num. obs: 26403 / % possible obs: 99.7 % / Rmerge(I) obs: 0.226 | ||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE CONSISTS IN AN ARRANGEMENT OF ORDERED AND DISORDERED LAYERS RESULTING IN GAPS BETWEEN ORDERED MOLECULES. ALTHOUGH NO MOLECULES ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE CONSISTS IN AN ARRANGEMENT OF ORDERED AND DISORDERED LAYERS RESULTING IN GAPS BETWEEN ORDERED MOLECULES. ALTHOUGH NO MOLECULES ARE MODELLED WITHIN THIS EMPTY LAYER, MAD DATA FROM SEMET-PRUA CRYSTALS INDICATES THAT PROTEIN ELECTRON DENSITY EXISTS WITHING THESE GAPS AND SUGGESTS A MOTION OF THE ENTIRE LAYER.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.091 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→39.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.503→2.568 Å / Total num. of bins used: 20
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