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Yorodumi- PDB-1lsj: Crystal Structure of the E110Q Mutant of L-3-Hydroxyacyl-CoA Dehy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lsj | ||||||
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Title | Crystal Structure of the E110Q Mutant of L-3-Hydroxyacyl-CoA Dehydrogenase in Complex with NAD | ||||||
Components | 3-HYDROXYACYL-COA DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | Function and homology information Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / fatty acid beta-oxidation / regulation of insulin secretion / NAD+ binding ...Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / fatty acid beta-oxidation / regulation of insulin secretion / NAD+ binding / negative regulation of insulin secretion / response to activity / response to insulin / positive regulation of cold-induced thermogenesis / transferase activity / mitochondrial matrix / response to xenobiotic stimulus / mitochondrion / nucleoplasm / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Barycki, J.J. / Banaszak, L.J. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the E110Q Mutant of L-3-Hydroxyacyl-CoA Dehydrogenase in Complex with NAD Authors: Barycki, J.J. / Banaszak, L.J. #1: Journal: Biochemistry / Year: 1999 Title: BIOCHEMICAL CHARACTERIZATION AND CRYSTAL STRUCTURE DETERMINATION OF HUMAN HEART SHORT CHAIN L-3-HYDROXYACYL-COA DEHYDROGENASE PROVIDE INSIGHTS INTO CATALYTIC MECHANISM Authors: Barycki, J.J. / O'Brien, L.K. / Bratt, J.M. / Zhang, R. / Sanishvili, R. / Strauss, A.W. / Banaszak, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lsj.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lsj.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/1lsj ftp://data.pdbj.org/pub/pdb/validation_reports/ls/1lsj | HTTPS FTP |
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-Related structure data
Related structure data | 3hadS 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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Unit cell |
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Details | biologically relevant dimer contained within the asymmetric unit |
-Components
#1: Protein | Mass: 32867.730 Da / Num. of mol.: 2 / Mutation: E110Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HCDH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: Q16836, 3-hydroxyacyl-CoA dehydrogenase #2: Chemical | #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: 2.75 Å3/Da / Density % sol: 55.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50 mM N-[2-ACETAMIDO]-2-IMINODIACETIC ACID WITHIN THE PRECIPITANT RANGE OF 14% TO 19% POLYETHYLENE GLYCOL 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 29, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→28 Å / Num. all: 25976 / Num. obs: 25717 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.77 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.75 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 7.2 / Num. unique all: 2527 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HAD Resolution: 2.5→26.7 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.1103 Å2 / ksol: 0.32982 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→26.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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