+Open data
-Basic information
Entry | Database: PDB / ID: 1bpw | ||||||
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Title | BETAINE ALDEHYDE DEHYDROGENASE FROM COD LIVER | ||||||
Components | PROTEIN (ALDEHYDE DEHYDROGENASE) | ||||||
Keywords | OXIDOREDUCTASE / ALDEHYDE OXIDATION / NAD COMPLEX | ||||||
Function / homology | Function and homology information 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / carnitine biosynthetic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / cytosol Similarity search - Function | ||||||
Biological species | Gadus callarias (Baltic cod) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Johansson, K. / El Ahmad, M. / Ramaswamy, S. / Hjelmqvist, L. / Jornvall, H. / Eklund, H. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Structure of betaine aldehyde dehydrogenase at 2.1 A resolution. Authors: Johansson, K. / El-Ahmad, M. / Ramaswamy, S. / Hjelmqvist, L. / Jornvall, H. / Eklund, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bpw.cif.gz | 379.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bpw.ent.gz | 311.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/1bpw ftp://data.pdbj.org/pub/pdb/validation_reports/bp/1bpw | HTTPS FTP |
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-Related structure data
Related structure data | 1a4sSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 54422.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: NAD COMPLEX / Source: (natural) Gadus callarias (Baltic cod) / Organ: LIVER / References: UniProt: P56533, betaine-aldehyde dehydrogenase #2: Chemical | ChemComp-NAD / #3: 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: 2.59 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 287 K / pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED AT 14 DEGREES FROM 20% PEG 4000, 9.5% ISOPROPANOL, 100 MM HEPES, PH 7.5, temperature 287K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 14 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 275 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 15, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→80 Å / Num. obs: 49784 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 12 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.8→2.98 Å / Mean I/σ(I) obs: 1.6 / % possible all: 88.5 |
Reflection | *PLUS Rmerge(I) obs: 0.124 |
Reflection shell | *PLUS % possible obs: 88.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A4S Resolution: 2.8→80 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 1565193.26 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 38.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→80 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.39 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.371 |