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Yorodumi- PDB-5n5s: Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Phys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n5s | ||||||
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Title | Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Physcomitrella patens in complex with NADP+ | ||||||
Components | Aldehyde dehydrogenase 21 (ALDH21) | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / succinic semialdehyde dehydrogenase / NADP+ binding | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (NADP+) / lactaldehyde dehydrogenase (NAD+) activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Physcomitrella patens subsp. patens (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kopecny, D. / Vigouroux, A. / Briozzo, P. / Morera, S. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Plant J. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n5s.cif.gz | 758.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n5s.ent.gz | 634.5 KB | Display | PDB format |
PDBx/mmJSON format | 5n5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n5s_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5n5s_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5n5s_validation.xml.gz | 65.5 KB | Display | |
Data in CIF | 5n5s_validation.cif.gz | 89.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/5n5s ftp://data.pdbj.org/pub/pdb/validation_reports/n5/5n5s | HTTPS FTP |
-Related structure data
Related structure data | 5mz5SC 5mz8C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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.) Physcomitrella patens subsp. patens (plant) Gene: PHYPADRAFT_215149 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A9SS48 #2: Chemical | ChemComp-NAP / #3: Chemical | #4: 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: 2.19 Å3/Da / Density % sol: 43.76 % |
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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, 1 mM NADP+; precipitant solution: 35% (w/v) PEG 2000-MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 91956 / % possible obs: 99.5 % / Redundancy: 12.9 % / Biso Wilson estimate: 68.55 Å2 / CC1/2: 0.999 / Rsym value: 0.099 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.3→2.43 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 14371 / CC1/2: 0.772 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MZ5 Resolution: 2.3→46.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.285 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.194
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Displacement parameters | Biso mean: 83.67 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→46.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 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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