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Yorodumi- PDB-6iun: Crystal structure of enoyl-CoA hydratase (ECH) from Ralstonia eut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iun | ||||||
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Title | Crystal structure of enoyl-CoA hydratase (ECH) from Ralstonia eutropha H16 in complex with NAD | ||||||
Components | Enoyl-CoA hydratase/Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase | ||||||
Keywords | OXIDOREDUCTASE / Enoyl-CoA hydratase / Ralstonia eutropha H16 | ||||||
Function / homology | Function and homology information 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / fatty acid beta-oxidation / NAD+ binding / isomerase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Cupriavidus necator (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Son, H.F. / Kim, K.J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of enoyl-CoA hydratase from Ralstonia eutropha H16 Authors: Son, H.F. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iun.cif.gz | 276.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iun.ent.gz | 221.9 KB | Display | PDB format |
PDBx/mmJSON format | 6iun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iun_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6iun_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6iun_validation.xml.gz | 52.8 KB | Display | |
Data in CIF | 6iun_validation.cif.gz | 72.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/6iun ftp://data.pdbj.org/pub/pdb/validation_reports/iu/6iun | HTTPS FTP |
-Related structure data
Related structure data | 6iumSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 75857.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (bacteria) Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: H16_A1526 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0KBG3 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: 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: 2.79 Å3/Da / Density % sol: 55.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 200 mM Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→92.64 Å / Num. obs: 66134 / % possible obs: 97.8 % / Redundancy: 5.1 % / Rsym value: 0.128 / Net I/σ(I): 36.91 |
Reflection shell | Resolution: 2.38→2.44 Å / Num. unique obs: 3181 / Rsym value: 0.312 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IUM Resolution: 2.38→92.63 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.927 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / ESU R Free: 0.25 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.61 Å2 / Biso mean: 49.546 Å2 / Biso min: 18.91 Å2
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Refinement step | Cycle: final / Resolution: 2.38→92.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.379→2.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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