+Open data
-Basic information
Entry | Database: PDB / ID: 6cl4 | ||||||
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Title | LipC12 - Lipase from metagenomics | ||||||
Components | Lipase C12 | ||||||
Keywords | HYDROLASE / Lipase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Iulek, J. / Martini, V.P. / Krieger, N. / Glogauer, A. / Souza, E.M. | ||||||
Citation | Journal: N Biotechnol / Year: 2019 Title: Structure solution and analyses of the first true lipase obtained from metagenomics indicate potential for increased thermostability. Authors: Martini, V.P. / Krieger, N. / Glogauer, A. / Souza, E.M. / Iulek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cl4.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cl4.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 6cl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cl4_validation.pdf.gz | 423.6 KB | Display | wwPDB validaton report |
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Full document | 6cl4_full_validation.pdf.gz | 424.8 KB | Display | |
Data in XML | 6cl4_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 6cl4_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/6cl4 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/6cl4 | HTTPS FTP |
-Related structure data
Related structure data | 1ex9S 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
#1: Protein | Mass: 33433.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: lipc12 / Production host: Escherichia coli (E. coli) / References: UniProt: G1APT8, triacylglycerol lipase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.4 % / Description: needles |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.0 M sodium formate and 0.1 M bis-tris propane, pH 7.0 using a protein concentration of 10 mg / mL. Crystals grown for ten weeks |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: nitrogen stream |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→58.5 Å / Num. obs: 10489 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 8.82 % / Rrim(I) all: 0.14 / Net I/σ(I): 18.91 |
Reflection shell | Resolution: 2.64→2.72 Å / Redundancy: 8.38 % / Mean I/σ(I) obs: 4.29 / Num. unique obs: 851 / Rrim(I) all: 0.641 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EX9 Resolution: 2.64→48.175 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.63
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→48.175 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.5125 Å / Origin y: 21.2 Å / Origin z: 22.0314 Å
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Refinement TLS group | Selection details: chain A |