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Yorodumi- PDB-4j0e: Crystal structure of 3-hydroxyacyl-CoA dehydrogenase from Caenorh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j0e | ||||||
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Title | Crystal structure of 3-hydroxyacyl-CoA dehydrogenase from Caenorhadbitis elegans in P1 space group | ||||||
Components | Probable 3-hydroxyacyl-CoA dehydrogenase F54C8.1 | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / dehydrogenase / fatty acid beta-oxidation / NADH binding / mitochondrial matrix | ||||||
Function / homology | Function and homology information 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / fatty acid beta-oxidation / NAD+ binding / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Xu, Y. / Sun, F. / Zhai, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Purification, crystallization and preliminary crystallographic analysis of 3-hydroxyacyl-CoA dehydrogenase from Caenorhabditis elegans. Authors: Xu, Y. / Sun, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j0e.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j0e.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 4j0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/4j0e ftp://data.pdbj.org/pub/pdb/validation_reports/j0/4j0e | HTTPS FTP |
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-Related structure data
Related structure data | 4j0fC 3hadS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 34709.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F54C8.1 / Plasmid: pEXS-CG (reconstructed plasmid based on pET-22b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P34439, 3-hydroxyacyl-CoA dehydrogenase #2: 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: 2.28 Å3/Da / Density % sol: 46.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 21% PEG 3350, 0.2M sodium chloride, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→54.04 Å / Num. all: 80630 / Num. obs: 77082 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.31 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HAD Resolution: 1.6→54.04 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.682 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.735 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→54.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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