+Open data
-Basic information
Entry | Database: PDB / ID: 6khl | |||||||||
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Title | Lipase (Blocked form) | |||||||||
Components | Hydrolase, alpha/beta domain protein | |||||||||
Keywords | HYDROLASE / lipase | |||||||||
Function / homology | Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / hydrolase activity / (2~{R})-1-phenylpropan-2-ol / DI(HYDROXYETHYL)ETHER / Hydrolase, alpha/beta domain protein Function and homology information | |||||||||
Biological species | Cutibacterium acnes HL110PA4 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 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 lipase 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 | 6khl.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6khl.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 6khl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/6khl ftp://data.pdbj.org/pub/pdb/validation_reports/kh/6khl | 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: 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 | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PEG / #5: 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: 2.53 Å3/Da / Density % sol: 51.45 % |
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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: 7A (6B, 6C1) / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 89922 / % possible obs: 98.7 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.02 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.21 / Num. unique obs: 3970 / Rpim(I) all: 0.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→31.91 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.036 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.07 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: 65.88 Å2 / Biso mean: 13.141 Å2 / Biso min: 6.15 Å2
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Refinement step | Cycle: final / Resolution: 1.6→31.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.638 Å / Rfactor Rfree error: 0
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