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Yorodumi- PDB-3hdh: PIG HEART SHORT CHAIN L-3-HYDROXYACYL COA DEHYDROGENASE REVISITED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hdh | ||||||
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Title | PIG HEART SHORT CHAIN L-3-HYDROXYACYL COA DEHYDROGENASE REVISITED: SEQUENCE ANALYSIS AND CRYSTAL STRUCTURE DETERMINATION | ||||||
Components | PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE) | ||||||
Keywords | OXIDOREDUCTASE / BETA OXIDATION / SCHAD / CATALYTIC ACTIVITY: L-3-HYDROXYACYL-COA + NAD(+) = 3-OXOACYL-COA + NADH | ||||||
Function / homology | Function and homology information Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-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 hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / fatty acid beta-oxidation / regulation of insulin secretion / NAD+ binding / positive regulation of cold-induced thermogenesis / mitochondrial matrix / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Barycki, J.J. / O'Brien, L.K. / Birktoft, J.J. / Strauss, A.W. / Banaszak, L.J. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Pig heart short chain L-3-hydroxyacyl-CoA dehydrogenase revisited: sequence analysis and crystal structure determination. Authors: Barycki, J.J. / O'Brien, L.K. / Birktoft, J.J. / Strauss, A.W. / Banaszak, L.J. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987 Title: Structure of L-3-Hydroxyacyl-Coenzyme a Dehydrogenase: Preliminary Chain Tracing at 2.8-A Resolution Authors: Birktoft, J.J. / Holden, H.M. / Hamlin, R. / Xuong, N.H. / 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 | 3hdh.cif.gz | 167.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hdh.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hdh ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hdh | 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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2 |
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Unit cell |
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Details | UNUSUAL SITUATION OF 3 SUBUNITS CONTAINED WITHIN THE ASYMMETRIC UNIT FOR A DIMERIC ENZYME. |
-Components
#1: Protein | Mass: 32831.719 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: HEART / Organelle: MITOCHONDRIALMitochondrion References: UniProt: P00348, 3-hydroxyacyl-CoA dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58 % / Description: USED DIMER AS A PROBE. | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: 10 MM TRIS, PH 8.0, + 1MM DTT + 11-14% PEG 6K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: gel filtration | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Wavelength: 1.54 |
Detector | Date: Jan 1, 1985 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 28840 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 58.7 Å2 / Rsym value: 0.046 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.8→2.97 Å / % possible all: 85 |
Reflection | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.046 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HAD Resolution: 2.8→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 6104754.86 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 Details: BULK SOLVENT MODEL USED POOR ELECTRON DENSITY OBSERVED FOR THIRD SUBUNIT (SUBUNIT C). THREE BREAKS WERE OBSERVED IN THE DENSITY AND SEVERAL RESIDUES HAVE BEEN ASSIGNED OCCUPANCIES OF 0.5
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Displacement parameters | Biso mean: 62.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 1 / % reflection Rfree: 4.9 % / Rfactor obs: 0.223 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 62.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.329 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.306 |