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Yorodumi- PDB-5a2d: CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH ... -
+Open data
-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 | ||||||
Components | (BETAINE ALDEHYDE DEHYDROGENASE, ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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: 1.98 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 | 5a2d.cif.gz | 783.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a2d.ent.gz | 653.4 KB | Display | PDB format |
PDBx/mmJSON format | 5a2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/5a2d ftp://data.pdbj.org/pub/pdb/validation_reports/a2/5a2d | HTTPS FTP |
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-Related structure data
Related structure data | 4v3fC 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, ... , 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.) SPINACIA OLERACEA (spinach) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P17202, betaine-aldehyde dehydrogenase #2: Protein | | Mass: 54343.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P17202, betaine-aldehyde dehydrogenase #3: Protein | | Mass: 54359.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P17202, betaine-aldehyde dehydrogenase |
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-Non-polymers , 7 types, 682 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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