+Open data
-Basic information
Entry | Database: PDB / ID: 5abm | ||||||
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Title | Sheep aldehyde dehydrogenase 1A1 | ||||||
Components | RETINAL DEHYDROGENASE 1 | ||||||
Keywords | OXIDOREDUCTASE / OXIDATION-REDUCTION PROCESS / ACTIVITY | ||||||
Function / homology | Function and homology information fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinol metabolic process / retinoid metabolic process / NAD binding / axon / synapse / cytosol Similarity search - Function | ||||||
Biological species | OVIS ARIES (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Koch, M.F. / Harteis, S. / Blank, I.D. / Pestel, G. / Tietze, L.F. / Ochsenfeld, C. / Schneider, S. / Sieber, S.A. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues. Authors: Koch, M.F. / Harteis, S. / Blank, I.D. / Pestel, G. / Tietze, L.F. / Ochsenfeld, C. / Schneider, S. / Sieber, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5abm.cif.gz | 780.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5abm.ent.gz | 655.6 KB | Display | PDB format |
PDBx/mmJSON format | 5abm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5abm_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 5abm_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5abm_validation.xml.gz | 84.2 KB | Display | |
Data in CIF | 5abm_validation.cif.gz | 122.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/5abm ftp://data.pdbj.org/pub/pdb/validation_reports/ab/5abm | HTTPS FTP |
-Related structure data
Related structure data | 5ac0C 5ac1C 5ac2C 4x4lS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8264, 0.000412, 0.5632), Vector: |
-Components
#1: Protein | Mass: 54754.391 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-501 Source method: isolated from a genetically manipulated source Source: (gene. exp.) OVIS ARIES (sheep) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51977, retinal dehydrogenase #2: Chemical | ChemComp-TXE / [[( #3: Chemical | ChemComp-MG / #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: 2.62 Å3/Da / Density % sol: 26.2 % / Description: NONE |
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Crystal grow | Temperature: 277 K Details: 100 MM BIS-TRIS, PH 6.0, 4.5-7% PEG5000, 150=225MM MGCL2, 4DEGREE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→51.8 Å / Num. obs: 249604 / % possible obs: 99.7 % / Observed criterion σ(I): 12.6 / Redundancy: 6.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.1 / % possible all: 97.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4X4L Resolution: 1.7→151.85 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.268 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.184 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→151.85 Å
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Refine LS restraints |
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