+Open data
-Basic information
Entry | Database: PDB / ID: 4y9l | |||||||||
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Title | Crystal Structure of Caenorhabditis elegans ACDH-11 | |||||||||
Components | Protein ACDH-11, isoform b | |||||||||
Keywords | OXIDOREDUCTASE / Acyl-CoA dehydrogenase | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / adaptive thermogenesis / oxidoreductase activity, acting on the CH-CH group of donors / fatty acid metabolic process / fatty acid binding / nucleotide binding Similarity search - Function | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | |||||||||
Authors | Li, Z.J. / Zhai, Y.J. / Zhang, K. / Sun, F. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell / Year: 2015 Title: Acyl-CoA Dehydrogenase Drives Heat Adaptation by Sequestering Fatty Acids Authors: Ma, D.K. / Li, Z. / Lu, A.Y. / Sun, F. / Chen, S. / Rothe, M. / Menzel, R. / Sun, F. / Horvitz, H.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y9l.cif.gz | 505.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y9l.ent.gz | 415 KB | Display | PDB format |
PDBx/mmJSON format | 4y9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/4y9l ftp://data.pdbj.org/pub/pdb/validation_reports/y9/4y9l | HTTPS FTP |
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-Related structure data
Related structure data | 4y9jC 3djlS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 65840.109 Da / Num. of mol.: 2 / Fragment: UNP residues 10-602 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: acdh-11, CELE_Y45F3A.3, Y45F3A.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q3T978, UniProt: Q9XWZ2*PLUS, very-long-chain acyl-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: 2.8 Å3/Da / Density % sol: 56.14 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 3350, Tris, magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99985 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99985 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. all: 67044 / Num. obs: 66307 / % possible obs: 98.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.11 / Net I/av σ(I): 39.4 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.27→2.31 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 4.1 / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DJL Resolution: 2.27→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 17.454 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 137.96 Å2 / Biso mean: 52.063 Å2 / Biso min: 25.76 Å2
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Refinement step | Cycle: final / Resolution: 2.27→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.329 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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