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Yorodumi- PDB-4ids: Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ids | ||||||
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Title | Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis | ||||||
Components | Delta-1-pyrroline-5-carboxylate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / PruA / delta-pyrroline-5-carboxylic dehydrogenase / aldehyde dehydrogenase / pyrroline-5-carboxylate dehydrogenase / pyrroline-5-carboxylate / dehydrogenation | ||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Lagautriere, T. / Bashiri, G. / Baker, E.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ids.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ids.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ids.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ids_validation.pdf.gz | 427.7 KB | Display | wwPDB validaton report |
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Full document | 4ids_full_validation.pdf.gz | 431.6 KB | Display | |
Data in XML | 4ids_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 4ids_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/4ids ftp://data.pdbj.org/pub/pdb/validation_reports/id/4ids | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 61210.691 Da / Num. of mol.: 1 / Mutation: G505D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1187 / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): Mc2 4517 References: UniProt: I6X0K4, UniProt: O50443*PLUS, EC: 1.5.1.12 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.25 Å3/Da / Density % sol: 80.33 % |
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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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | |||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 9, 2011 | |||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 2→19.95 Å / Num. all: 99327 / Num. obs: 99327 / % possible obs: 99.7 % | |||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→19.95 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.899 / SU B: 3.139 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 27.748 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.038→2.09 Å / Total num. of bins used: 20
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