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Yorodumi- PDB-1ex9: CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LIPASE COMPLEXED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ex9 | ||||||
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Title | CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LIPASE COMPLEXED WITH RC-(RP,SP)-1,2-DIOCTYLCARBAMOYL-GLYCERO-3-O-OCTYLPHOSPHONATE | ||||||
Components | LACTONIZING LIPASE | ||||||
Keywords | HYDROLASE / Lipase / alpha-beta hydrolase fold / Pseudomonas / phosphonate inhibitor | ||||||
Function / homology | Function and homology information protein transport by the Sec complex / lipase activity / protein secretion by the type II secretion system / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Nardini, M. / Lang, D.A. / Liebeton, K. / Jaeger, K.-E. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Crystal structure of pseudomonas aeruginosa lipase in the open conformation. The prototype for family I.1 of bacterial lipases. Authors: Nardini, M. / Lang, D.A. / Liebeton, K. / Jaeger, K.E. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ex9.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ex9.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ex9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ex9_validation.pdf.gz | 664.2 KB | Display | wwPDB validaton report |
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Full document | 1ex9_full_validation.pdf.gz | 669.7 KB | Display | |
Data in XML | 1ex9_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 1ex9_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/1ex9 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/1ex9 | 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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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 30160.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PEL11 / Production host: Pseudomonas aeruginosa (bacteria) / Strain (production host): PAC1R / References: UniProt: P26876, triacylglycerol lipase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-OCP / |
#4: 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: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: MPD, calcium chloride, citrate , pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 285K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 29, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→28.55 Å / Num. all: 34304 / Num. obs: 8772 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.119 |
Reflection shell | Resolution: 2.54→28.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.336 / Num. unique all: 1056 / % possible all: 98.2 |
Reflection | *PLUS Num. measured all: 34304 |
Reflection shell | *PLUS % possible obs: 98.2 % / Mean I/σ(I) obs: 4.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→28.55 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.54→28.55 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.193 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |