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- PDB-5a2d: CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a2d | ||||||
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Title | CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH SHOWING A THIOHEMIACETAL WITH BETAINE ALDEHYDE | ||||||
![]() | (BETAINE ALDEHYDE DEHYDROGENASE, ...) x 3 | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase (NAD+) activity / cellular aldehyde metabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glycine betaine biosynthetic process from choline / cellular detoxification of aldehyde ...4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase (NAD+) activity / cellular aldehyde metabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glycine betaine biosynthetic process from choline / cellular detoxification of aldehyde / potassium ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zarate-Romero, A. / Munoz-Clares, R.A. | ||||||
![]() | ![]() Title: Reversible, Partial Inactivation of Plant Betaine Aldehyde Dehydrogenase by Betaine Aldehyde: Mechanism and Possible Physiological Implications. Authors: Zarate-Romero, A. / Murillo-Melo, D.S. / Mujica-Jimenez, C. / Montiel, C. / Munoz-Clares, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 783.8 KB | Display | ![]() |
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PDB format | ![]() | 653.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 518.4 KB | Display | ![]() |
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Full document | ![]() | 583 KB | Display | |
Data in XML | ![]() | 82.7 KB | Display | |
Data in CIF | ![]() | 113.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v3fC ![]() 4a0mS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-BETAINE ALDEHYDE DEHYDROGENASE, ... , 3 types, 4 molecules ABCD
#1: Protein | Mass: 54327.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THIOHEMIACETAL BOND BETWEEN BETAINE ALDEHYDE AND C450 IN CHAIN A AND B Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 54343.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | | Mass: 54359.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 7 types, 682 molecules ![](data/chem/img/CHT.gif)
![](data/chem/img/ETX.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/AE3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ETX.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/AE3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-K / #7: Chemical | ChemComp-PG4 / | #8: Chemical | ChemComp-AE3 / | #9: Chemical | ChemComp-GOL / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.47 % / Description: NONE |
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Crystal grow | pH: 7 Details: POLYETHYLENE GLYCOL 3350 20% (V/V), 0.2 M MAGNESIUM FORMATE DIHYDRATE, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 12, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→28.7 Å / Num. obs: 126693 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.62 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4A0M Resolution: 1.98→28.7 Å / SU ML: 0.25 / σ(F): 1.96 / Phase error: 27.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→28.7 Å
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Refine LS restraints |
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LS refinement shell |
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