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Yorodumi- PDB-4kjx: Crystal Structure of the complex of three phase partition treated... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kjx | ||||||
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Title | Crystal Structure of the complex of three phase partition treated lipase from Thermomyces lanuginosa with Lauric acid and P-nitrobenzaldehyde (PNB) at 2.1 resolution | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process Similarity search - Function | ||||||
Biological species | Thermomyces lanuginosus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kumar, M. / Mukherjee, J. / Gupta, M.N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of the complex of three phase partition treated lipase from Thermomyces lanuginosa with Lauric acid and P-nitrobenzaldehyde (PNB) at 2.1 resolution Authors: Kumar, M. / Mukherjee, J. / Gupta, M.N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kjx.cif.gz | 123.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kjx.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 4kjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/4kjx ftp://data.pdbj.org/pub/pdb/validation_reports/kj/4kjx | HTTPS FTP |
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-Related structure data
Related structure data | 4ea6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 29342.484 Da / Num. of mol.: 2 / Fragment: UNP residues 23-291 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase #2: Sugar | |
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-Non-polymers , 6 types, 280 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-XXH / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, O.1M Nacl, 1.6M Ammonium sulphate , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 18, 2012 / Details: Mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 98715 / Num. obs: 48911 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 40.5 Å2 / Rsym value: 0.086 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2 / Num. unique all: 48911 / Rsym value: 0.443 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EA6 Resolution: 2.1→45.83 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.994 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 35.951 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→45.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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