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Open data
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Basic information
Entry | Database: PDB / ID: 1dxy | ||||||
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Title | STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE | ||||||
![]() | D-2-HYDROXYISOCAPROATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / D-2-HYDROXYCARBOXYLATE DEHYDROGENASE / D-LACTATE DEHYDROGENASE | ||||||
Function / homology | ![]() Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dengler, U. / Niefind, K. / Kiess, M. / Schomburg, D. | ||||||
![]() | ![]() Title: Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. Authors: Dengler, U. / Niefind, K. / Kiess, M. / Schomburg, D. #1: ![]() Title: Crystallization and Preliminary Characterization of Crystals of D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei Authors: Niefind, K. / Hecht, H.J. / Schomburg, D. #2: ![]() Title: Roentgenkristallographische Untersuchungen an Drei Mikrobiellen Enzymen: D-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Casei L-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus ...Title: Roentgenkristallographische Untersuchungen an Drei Mikrobiellen Enzymen: D-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Casei L-2-Hydroxyisocaproat-Dehydrogenase Aus Lactobacillus Confusus Alkalische Protease Aus Bacillus Alcalophilus/Variante Q59R Authors: Niefind, K. #3: ![]() Title: Potential of R-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei for Stereospecific Reductions Authors: Kallwass, H.K.W. #4: ![]() Title: Cloning, Sequencing and Expression in Escherichia Coli of the D-2-Hydroxyisocaproate Dehydrogenase Gene of Lactobacillus Casei Authors: Lerch, H.P. / Blocker, H. / Kallwass, H. / Hoppe, J. / Tsai, H. / Collins, J. #5: ![]() Title: Crystallization and Molecular Properties of D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei Authors: Kallwass, H. / Tsai, H. / Schuette, H. #6: ![]() Title: D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei. A New Enzyme Suitable for Stereospecific Reduction of 2-Ketocarboxylic Acids Authors: Hummel, W. / Schuette, H. / Kula, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.6 KB | Display | ![]() |
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PDB format | ![]() | 63.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gdhS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | D-HICDH IS A DIMER OF IDENTICAL SUBUNITS, WHICH OCCUPIES A SPECIAL POSITION IN THE INVESTIGATED CRYSTALS. |
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Components
#1: Protein | Mass: 36929.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17584, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor | ||||||||||
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#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-COI / | #5: Water | ChemComp-HOH / | Nonpolymer details | 2-OXOISOCAPROATE (OIC 337) AND A SULFATE ION (SO4 338) ARE MUTUALLY EXCLUSIVELY BOUND IN THE ACTIVE ...2-OXOISOCAPR | Sequence details | A CONTACT IS OBSERVED BETWEEN THE SIDE CHAINS OF ASP 266 AND ASP 278. CHEMICAL PROTEIN SEQUENCING ...A CONTACT IS OBSERVED BETWEEN THE SIDE CHAINS OF ASP 266 AND ASP 278. CHEMICAL PROTEIN SEQUENCING | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 7 Details: 1.9 M AMMONIUM SULFATE, 50 MM CITRATE/PHOSPHATE BUFFER, 30 MM NAD+, 60 MM 4-METHYL-2-OXOPENTANOATE, PH 7.0, 277 K; ENZYME CONCENTRATION 10 MG/ML. | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Niefind, K., (1994) J.Mol.Biol., 240, 400. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 1994 / Details: MIRROR OPTICS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→12.1 Å / Num. obs: 53838 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.089 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.86→2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.48 / % possible all: 86.9 |
Reflection | *PLUS Num. measured all: 314570 / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 86.9 % / Rmerge(I) obs: 0.48 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: BACKBONE AND C-BETA ATOMS OF D-GLYCERATE DEHYDROGENASE (PDB ENTRY 1GDH) Resolution: 1.86→12.1 Å / σ(F): 0
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Displacement parameters | Biso mean: 31.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å / Luzzati sigma a obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→12.1 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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