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Open data
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Basic information
Entry | Database: PDB / ID: 6khk | |||||||||
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Title | Lipase (Closed form) | |||||||||
![]() | Hydrolase, alpha/beta domain protein![]() | |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kim, H.J. / Kwon, A.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Closed, blocked, and open states of lysophospholipase from type II Cutibacterium acnes Authors: Kim, H.J. / Lee, B.J. / Kwon, A.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.9 KB | Display | ![]() |
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PDB format | ![]() | 108.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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: 34471.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HMPREF9578_02569 / Production host: ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.71 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30 % (w/v) PEG 8K and 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.75→50 Å / Num. obs: 63275 / % possible obs: 92.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 0.295 / Num. unique obs: 3120 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.3 Å2 / Biso mean: 16.791 Å2 / Biso min: 6.38 Å2
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Refinement step | Cycle: final / Resolution: 1.75→38.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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