+Open data
-Basic information
Entry | Database: PDB / ID: 4oe6 | ||||||
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Title | Crystal Structure of Yeast ALDH4A1 | ||||||
Components | Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / PUT2P / ALDEHYDE DEHYDROGENASE / ALDH4A1 / ROSSMANN FOLD / NAD / mitochondria | ||||||
Function / homology | Function and homology information 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / glutamate biosynthetic process / L-glutamate gamma-semialdehyde dehydrogenase / mitochondrial inner membrane / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å | ||||||
Authors | Tanner, J.J. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structural Studies of Yeast Delta (1)-Pyrroline-5-carboxylate Dehydrogenase (ALDH4A1): Active Site Flexibility and Oligomeric State. Authors: Pemberton, T.A. / Srivastava, D. / Sanyal, N. / Henzl, M.T. / Becker, D.F. / Tanner, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oe6.cif.gz | 384.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oe6.ent.gz | 313.5 KB | Display | PDB format |
PDBx/mmJSON format | 4oe6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/4oe6 ftp://data.pdbj.org/pub/pdb/validation_reports/oe/4oe6 | HTTPS FTP |
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-Related structure data
Related structure data | 4oe4C 4oe5C 3v9jS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 65111.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: PUT2, YHR037W / Plasmid: pKA8H / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS References: UniProt: P07275, L-glutamate gamma-semialdehyde dehydrogenase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 8 - 14 % (w/v) polyethylene glycol (PEG) 3350, 0.1 M (NH4)2SO4, and 0.1 M Bis-Tris at pH 5.5 - 6.5. , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. obs: 88348 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.33 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.022 / Net I/σ(I): 10.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V9J Resolution: 1.951→40.474 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8711 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.43 Å2 / Biso mean: 27.6249 Å2 / Biso min: 8.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.951→40.474 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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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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