+Open data
-Basic information
Entry | Database: PDB / ID: 6khk | |||||||||
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Title | Lipase (Closed form) | |||||||||
Components | Hydrolase, alpha/beta domain protein | |||||||||
Keywords | HYDROLASE / Lipase | |||||||||
Function / homology | Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / hydrolase activity / Hydrolase, alpha/beta domain protein Function and homology information | |||||||||
Biological species | Cutibacterium acnes HL110PA4 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | |||||||||
Authors | Kim, H.J. / Kwon, A.R. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6khk.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6khk.ent.gz | 108.7 KB | Display | PDB format |
PDBx/mmJSON format | 6khk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6khk_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 6khk_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 6khk_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 6khk_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/6khk ftp://data.pdbj.org/pub/pdb/validation_reports/kh/6khk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Cutibacterium acnes HL110PA4 (bacteria) Gene: HMPREF9578_02569 / Production host: Escherichia coli (E. coli) / References: UniProt: E6DAE5 #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.5 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: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å |
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: 0.98 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→38.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.543 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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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