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Yorodumi- PDB-1lde: HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND N-FORMYL ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lde | ||||||
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Title | HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND N-FORMYL PIPERDINE | ||||||
Components | LIVER ALCOHOL DEHYDROGENASE | ||||||
Keywords | DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / FORMAMIDES / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinol metabolic process / retinoic acid metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Ramaswamy, S. / Plapp, B.V. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Binding of formamides to liver alcohol dehydrogenase. Authors: Ramaswamy, S. / Scholze, M. / Plapp, B.V. #1: Journal: Biochemistry / Year: 1997 Title: Flexibility of Liver Alcohol Dehydrogenase in Stereoselective Binding of 3-Butylthiolane 1-Oxides Authors: Cho, H. / Ramaswamy, S. / Plapp, B.V. #2: Journal: J.Biol.Chem. / Year: 1982 Title: Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Plapp, B.V. / Samama, J.P. / Branden, C.I. #3: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 A Resolution Authors: Eklund, H. / Samma, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A. #4: Journal: J.Mol.Biol. / Year: 1976 Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A Resolution Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lde.cif.gz | 300.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lde.ent.gz | 242.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lde_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1lde_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1lde_validation.xml.gz | 69.2 KB | Display | |
Data in CIF | 1lde_validation.cif.gz | 92.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/1lde ftp://data.pdbj.org/pub/pdb/validation_reports/ld/1lde | HTTPS FTP |
-Related 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: COMMERCIAL PREPARATION OF ENZYME FROM HORSE LIVER. CDNA SEQUENCE M64864 Source: (natural) Equus caballus (horse) / Cellular location: CYTOPLASM / Organ: LIVER / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-FPI / #5: 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: 2.35 Å3/Da / Density % sol: 47 % / Description: ISOMORPHOUS STRUCTURE WAS USED | ||||||||||||||||||||||||||||||
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Crystal grow | Method: batch dialysis / pH: 7 Details: PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 ...Details: PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 MM 3-BUTYLTHIOLANE 1-OXIDE. VERY CLOSE TO C-CENTERED ORTHORHOMBIC BUT SCALES VERY BADLY AS C222. SO THE SYMMETRY IS ACTUALLY P21., batch dialysis | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ / Method: microdialysis | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 94632 / % possible obs: 88.8 % / Redundancy: 2.1 % / Rsym value: 0.035 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 8.8 / Rsym value: 0.087 / % possible all: 77.2 |
Reflection | *PLUS Rmerge(I) obs: 0.035 |
Reflection shell | *PLUS % possible obs: 77.2 % / Rmerge(I) obs: 0.087 |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE STRUCTURE WAS REFINED THROUG OUT WITH LARGE NCS RESTRAINTS. WATER WAS ADDED AUTOMATICALLY BY THE PROGRAM ARP.
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Displacement parameters | Biso mean: 18.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: 'REFMAC' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |