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- PDB-5mz5: Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Phys... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mz5 | ||||||
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Title | Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Physcomitrella patens in its apoform | ||||||
![]() | ALDH21) | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold / succinic semialdehyde dehydrogenase / NADP+ binding | ||||||
Function / homology | ![]() glyceraldehyde-3-phosphate dehydrogenase (NADP+) / lactaldehyde dehydrogenase (NAD+) activity / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kopecny, D. / Koncitikova, R. / Briozzo, P. / Morera, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The ALDH21 gene found in lower plants and some vascular plants codes for a NADP(+) -dependent succinic semialdehyde dehydrogenase. Authors: Kopecna, M. / Vigouroux, A. / Vilim, J. / Koncitikova, R. / Briozzo, P. / Hajkova, E. / Jaskova, L. / von Schwartzenberg, K. / Sebela, M. / Morera, S. / Kopecny, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 742.2 KB | Display | ![]() |
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PDB format | ![]() | 616.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 494 KB | Display | ![]() |
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Full document | ![]() | 503.7 KB | Display | |
Data in XML | ![]() | 73.5 KB | Display | |
Data in CIF | ![]() | 105.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mz8C ![]() 5n5sC ![]() 2w8qS 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: 56637.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PHYPADRAFT_215149 / Plasmid: pCDFDuet / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: protein buffer: 20 mM Tris-HCl buffer pH 8.0, 100 mM NaCl and 2% (w/v) glycerol; precipitant solution: 30 % (w/v) PEG 2000-MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 120186 / % possible obs: 98.6 % / Redundancy: 6.41 % / Biso Wilson estimate: 36.94 Å2 / Rsym value: 0.139 / Net I/σ(I): 10.46 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 3.24 % / Mean I/σ(I) obs: 1.36 / Rsym value: 0.8 / % possible all: 91.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2W8Q Resolution: 2.15→48.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.165
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Displacement parameters | Biso mean: 34.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→48.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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