+Open data
-Basic information
Entry | Database: PDB / ID: 1dxy | ||||||
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Title | STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE | ||||||
Components | D-2-HYDROXYISOCAPROATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / D-2-HYDROXYCARBOXYLATE DEHYDROGENASE / D-LACTATE DEHYDROGENASE | ||||||
Function / homology | Function and homology information D-2-hydroxyacid dehydrogenase (NAD+) / D-lactate dehydrogenase activity / NAD binding Similarity search - Function | ||||||
Biological species | Lactobacillus casei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Dengler, U. / Niefind, K. / Kiess, M. / Schomburg, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 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: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary Characterization of Crystals of D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei Authors: Niefind, K. / Hecht, H.J. / Schomburg, D. #2: Journal: Thesis / Year: 1993 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: Journal: ENZYME.MICROB.TECHNOL. / Year: 1992 Title: Potential of R-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei for Stereospecific Reductions Authors: Kallwass, H.K.W. #4: Journal: Gene / Year: 1989 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: Journal: Fems Microbiol.Lett. / Year: 1987 Title: Crystallization and Molecular Properties of D-2-Hydroxyisocaproate Dehydrogenase from Lactobacillus Casei Authors: Kallwass, H. / Tsai, H. / Schuette, H. #6: Journal: Appl.Microbiol.Biotechnol. / Year: 1985 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dxy.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dxy.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dxy_validation.pdf.gz | 754.2 KB | Display | wwPDB validaton report |
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Full document | 1dxy_full_validation.pdf.gz | 756.8 KB | Display | |
Data in XML | 1dxy_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1dxy_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dxy ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dxy | HTTPS FTP |
-Related structure data
Related structure data | 1gdhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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. |
-Components
#1: Protein | Mass: 36929.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: POTENTIAL / Variant: SSP. PSEUDOPLANTARUM / Plasmid: PJLA601 / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 3 |
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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: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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