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Yorodumi- PDB-3iwk: Crystal structure of aminoaldehyde dehydrogenase 1 from Pisum sat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iwk | ||||||
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Title | Crystal structure of aminoaldehyde dehydrogenase 1 from Pisum sativum (PsAMADH1) | ||||||
Components | Aminoaldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / dimer / aminoaldehyde dehydrogenase / betaine aldehyde dehydrogenase / NAD | ||||||
Function / homology | Function and homology information 1-pyrroline dehydrogenase activity / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / nucleotide binding Similarity search - Function | ||||||
Biological species | Pisum sativum (garden pea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Kopecny, D. / Morera, S. / Briozzo, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural and functional characterization of plant aminoaldehyde dehydrogenase from Pisum sativum with a broad specificity for natural and synthetic aminoaldehydes. Authors: Tylichova, M. / Kopecny, D. / Morera, S. / Briozzo, P. / Lenobel, R. / Snegaroff, J. / Sebela, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iwk.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3iwk.ent.gz | 954.6 KB | Display | PDB format |
PDBx/mmJSON format | 3iwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/3iwk ftp://data.pdbj.org/pub/pdb/validation_reports/iw/3iwk | HTTPS FTP |
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-Related structure data
Related structure data | 3iwjC 1cw3S 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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Unit cell |
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-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 54868.746 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Gene: amadh1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8VWZ1, aminobutyraldehyde dehydrogenase |
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-Non-polymers , 5 types, 2041 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MRD / ( | #6: 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: 2.9 Å3/Da / Density % sol: 57.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 13% PEG 6000, 5% 2-methyl-2,4-pentanediol, 5mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. all: 291593 / Num. obs: 290858 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 40.72 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.06 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CW3 Resolution: 2.4→47.84 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.016 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 86.72 Å2 / Biso mean: 34.693 Å2 / Biso min: 14.36 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→47.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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