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Yorodumi- PDB-6kq9: A long chain secondary alcohol dehydrogenase of Micrococcus luteus -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kq9 | ||||||
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Title | A long chain secondary alcohol dehydrogenase of Micrococcus luteus | ||||||
Components | 3-hydroxybutyryl-CoA dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase | ||||||
Function / homology | Function and homology information 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity / NAD+ binding / fatty acid metabolic process Similarity search - Function | ||||||
Biological species | Micrococcus luteus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å | ||||||
Authors | Kim, H.J. / Kim, J.S. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2019 Title: Cofactor specificity engineering of a long-chain secondary alcohol dehydrogenase from Micrococcus luteus for redox-neutral biotransformation of fatty acids. Authors: Seo, E.J. / Kim, H.J. / Kim, M.J. / Kim, J.S. / Park, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kq9.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kq9.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/6kq9 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/6kq9 | HTTPS FTP |
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-Related structure data
Related structure data | 6kqbC 4dydS 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: 36857.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micrococcus luteus (bacteria) / Gene: GY12_10930 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085E1L0, UniProt: A0A4U1L6L9*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.65 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. obs: 19681 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 46.62 Å2 / Rrim(I) all: 0.119 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.25→2.29 Å / Num. unique obs: 954 / Rrim(I) all: 0.831 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DYD Resolution: 2.251→19.814 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.36 Å2 / Biso mean: 50.6014 Å2 / Biso min: 33.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.251→19.814 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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