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- PDB-6k8t: Crystal structure of C-domain with CoA of baterial malonyl-CoA re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k8t | ||||||
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Title | Crystal structure of C-domain with CoA of baterial malonyl-CoA reductase | ||||||
![]() | NAD-dependent epimerase/dehydratase:Short-chain dehydrogenase/reductase SDR | ||||||
![]() | OXIDOREDUCTASE / SDR domain | ||||||
Function / homology | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / nucleotide binding / COENZYME A / NAD-dependent epimerase/dehydratase:Short-chain dehydrogenase/reductase SDR![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kim, S. / Kim, K.-J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 279.7 KB | Display | ![]() |
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PDB format | ![]() | 222.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.3 MB | Display | ![]() |
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Full document | ![]() | 5.3 MB | Display | |
Data in XML | ![]() | 52.3 KB | Display | |
Data in CIF | ![]() | 75.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6k8sSC ![]() 6k8uC ![]() 6k8vC ![]() 6k8wC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: I603_0811 / Plasmid: pET28a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.31 % |
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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: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 135215 / % possible obs: 99.3 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Rrim(I) all: 0.088 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 6666 / CC1/2: 0.876 / Rpim(I) all: 0.134 / Rrim(I) all: 0.327 / % possible all: 98.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6K8S Resolution: 1.9→30.89 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.482 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107 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: 131.32 Å2 / Biso mean: 25.598 Å2 / Biso min: 7.34 Å2
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Refinement step | Cycle: final / Resolution: 1.9→30.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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