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Yorodumi- PDB-3rqs: Crystal Structure of human L-3- Hydroxyacyl-CoA dehydrogenase (EC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rqs | ||||||
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Title | Crystal Structure of human L-3- Hydroxyacyl-CoA dehydrogenase (EC1.1.1.35) from mitochondria at the resolution 2.0 A, Northeast Structural Genomics Consortium Target HR487, Mitochondrial Protein Partnership | ||||||
Components | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / PSI-biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Mitochondrial Protein Partnership / MPP | ||||||
Function / homology | Function and homology information Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of lauroyl-CoA to decanoyl-CoA-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 butanoyl-CoA to acetyl-CoA / Beta oxidation of lauroyl-CoA to decanoyl-CoA-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 / Mitochondrial protein degradation / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Kuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) / Mitochondrial Protein Partnership (MPP) | ||||||
Citation | Journal: To be published Title: Northeast Structural Genomics Consortium Target HR487 Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Shastry, R. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rqs.cif.gz | 266 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rqs.ent.gz | 214.4 KB | Display | PDB format |
PDBx/mmJSON format | 3rqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rqs_validation.pdf.gz | 450.2 KB | Display | wwPDB validaton report |
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Full document | 3rqs_full_validation.pdf.gz | 458 KB | Display | |
Data in XML | 3rqs_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 3rqs_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/3rqs ftp://data.pdbj.org/pub/pdb/validation_reports/rq/3rqs | HTTPS FTP |
-Related structure data
Related structure data | 1f0yS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36036.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HADH, HAD, HADHSC, SCHAD / Production host: Escherichia coli (E. coli) References: UniProt: Q16836, 3-hydroxyacyl-CoA dehydrogenase #2: Chemical | ChemComp-GOL / #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: 2.45 Å3/Da / Density % sol: 49.76 % |
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Crystal grow | Temperature: 277 K / Method: macrobatch under oil / pH: 4.2 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M Potassium phosphate dibasic (K2HPO4), 0.1M Sodium Citrate, 20% (w/v) PEG 4000, macrobatch ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M Potassium phosphate dibasic (K2HPO4), 0.1M Sodium Citrate, 20% (w/v) PEG 4000, macrobatch under oil, temperature 277KK |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 23, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 48661 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 25.61 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.94 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F0Y Resolution: 2.001→29.824 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.882 / SU ML: 0.23 / σ(F): 1.35 / Phase error: 18.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.875 Å2 / ksol: 0.363 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 200.42 Å2 / Biso mean: 30.092 Å2 / Biso min: 8.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.001→29.824 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Origin x: 21.9098 Å / Origin y: 66.1095 Å / Origin z: 106.1312 Å
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Refinement TLS group |
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