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Yorodumi- PDB-2qxu: Crystal Structure Analysis of the Bacillus subtilis lipase crysta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qxu | ||||||
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Title | Crystal Structure Analysis of the Bacillus subtilis lipase crystallized at pH 5.0 | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase fold / Lipid degradation / Secreted | ||||||
Function / homology | Function and homology information lipase activity / triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rajakumara, E. / Sankaranarayanan, R. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2008 Title: Structural basis for the remarkable stability of Bacillus subtilis lipase (Lip A) at low pH Authors: Rajakumara, E. / Acharya, P. / Ahmad, S. / Sankaranaryanan, R. / Rao, N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qxu.cif.gz | 283 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qxu.ent.gz | 230.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qxu_validation.pdf.gz | 481.9 KB | Display | wwPDB validaton report |
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Full document | 2qxu_full_validation.pdf.gz | 502.9 KB | Display | |
Data in XML | 2qxu_validation.xml.gz | 58.3 KB | Display | |
Data in CIF | 2qxu_validation.cif.gz | 82.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/2qxu ftp://data.pdbj.org/pub/pdb/validation_reports/qx/2qxu | HTTPS FTP |
-Related structure data
Related structure data | 2qxtC 1i6wS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 19182.643 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA / Plasmid: pET-21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37957, triacylglycerol lipase #2: Water | ChemComp-HOH / | |
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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: 2.05 Å3/Da / Density % sol: 40.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5 Details: 32% PEG 6000, 100mM Sodium acetate pH 5.0, 15mM Ammonium sulfate, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 25, 2003 / Details: mirrors |
Radiation | Monochromator: Osmic Mirror System / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 100779 / Num. obs: 96606 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.095 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 10050 / Rsym value: 0.23 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1I6W Resolution: 1.9→24.81 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 238428.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.8531 Å2 / ksol: 0.356685 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
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Xplor file |
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