+Open data
-Basic information
Entry | Database: PDB / ID: 6k8s | ||||||
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Title | Crystal structure of C-domain of baterial malonyl-CoA reductase | ||||||
Components | NAD-dependent epimerase/dehydratase:Short-chain dehydrogenase/reductase SDR | ||||||
Keywords | OXIDOREDUCTASE / SDR domain | ||||||
Function / homology | short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / NAD-dependent epimerase/dehydratase:Short-chain dehydrogenase/reductase SDR Function and homology information | ||||||
Biological species | Porphyrobacter dokdonensis DSW-74 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Kim, S. / Kim, K.-J. | ||||||
Citation | Journal: Environ.Microbiol. / Year: 2020 Title: Structural insight into bi-functional malonyl-CoA reductase. Authors: Son, H.F. / Kim, S. / Seo, H. / Hong, J. / Lee, D. / Jin, K.S. / Park, S. / 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 | 6k8s.cif.gz | 292.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k8s.ent.gz | 232.5 KB | Display | PDB format |
PDBx/mmJSON format | 6k8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/6k8s ftp://data.pdbj.org/pub/pdb/validation_reports/k8/6k8s | HTTPS FTP |
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-Related 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: 75705.797 Da / Num. of mol.: 2 / Fragment: SDR C domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyrobacter dokdonensis DSW-74 (bacteria) Gene: I603_0811 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1A7BFR5 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.03 Å3/Da / Density % sol: 59.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Li2SO4, HEPES |
-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: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 156374 / % possible obs: 97.8 % / Redundancy: 5.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Rsym value: 0.028 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.381 / Num. unique obs: 7610 / CC1/2: 0.736 / Rsym value: 0.187 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→29.86 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.307 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.101 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: 116.26 Å2 / Biso mean: 26.395 Å2 / Biso min: 8.55 Å2
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Refinement step | Cycle: final / Resolution: 1.8→29.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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