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Yorodumi- PDB-4v3f: Crystal structure of betaine aldehyde dehydrogenase from spinach ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v3f | ||||||
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Title | Crystal structure of betaine aldehyde dehydrogenase from spinach showing a thiohemiacetal with betaine aldehyde | ||||||
Components | (BETAINE ALDEHYDE DEHYDROGENASE, ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / BETAINE ALDEHYDE DEHYDROGENASE / ALDH10. | ||||||
Function / homology | Function and homology information 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / cellular aldehyde metabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / cellular detoxification of aldehyde ...4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / cellular aldehyde metabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / cellular detoxification of aldehyde / potassium ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | SPINACIA OLERACEA (spinach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å | ||||||
Authors | Zarate-Romero, A. / Munoz-Clares, R.A. | ||||||
Citation | Journal: Biochem.J. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v3f.cif.gz | 783.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v3f.ent.gz | 653.2 KB | Display | PDB format |
PDBx/mmJSON format | 4v3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/4v3f ftp://data.pdbj.org/pub/pdb/validation_reports/v3/4v3f | HTTPS FTP |
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-Related structure data
Related structure data | 5a2dC 4a0mS 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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1 |
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2 |
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Unit cell |
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-Components
-BETAINE ALDEHYDE DEHYDROGENASE, ... , 2 types, 4 molecules ABDC
#1: Protein | Mass: 54343.027 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17202, betaine-aldehyde dehydrogenase #2: Protein | | Mass: 54359.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17202, betaine-aldehyde dehydrogenase |
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-Non-polymers , 6 types, 685 molecules
#3: Chemical | ChemComp-IOD / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ETX / | #8: 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: 2.15 Å3/Da / Density % sol: 42.7 % / Description: NONE |
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Crystal grow | pH: 6.2 Details: AMMONIUM IODIDE 0.2 M, POLY ETHYLENE GLYCOL 3350 20% (W/V), PH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 13, 2014 |
Radiation | Monochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2→29 Å / Num. obs: 122131 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.3 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A0M Resolution: 1.998→28.968 Å / SU ML: 0.23 / σ(F): 1.96 / Phase error: 23.07 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.998→28.968 Å
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Refine LS restraints |
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LS refinement shell |
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