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Yorodumi- PDB-1k8q: CRYSTAL STRUCTURE OF DOG GASTRIC LIPASE IN COMPLEX WITH A PHOSPHO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k8q | ||||||
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Title | CRYSTAL STRUCTURE OF DOG GASTRIC LIPASE IN COMPLEX WITH A PHOSPHONATE INHIBITOR | ||||||
Components | Triacylglycerol lipase, gastric | ||||||
Keywords | HYDROLASE / APHA BETA HYDROLASE FOLD | ||||||
Function / homology | Function and homology information triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / intracellular membrane-bounded organelle / extracellular region Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Roussel, A. / Miled, N. / Berti-Dupuis, L. / Riviere, M. / Spinelli, S. / Berna, P. / Gruber, V. / Verger, R. / Cambillau, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of the open form of dog gastric lipase in complex with a phosphonate inhibitor. Authors: Roussel, A. / Miled, N. / Berti-Dupuis, L. / Riviere, M. / Spinelli, S. / Berna, P. / Gruber, V. / Verger, R. / Cambillau, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k8q.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k8q.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 1k8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k8q_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1k8q_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1k8q_validation.xml.gz | 36.6 KB | Display | |
Data in CIF | 1k8q_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/1k8q ftp://data.pdbj.org/pub/pdb/validation_reports/k8/1k8q | HTTPS FTP |
-Related structure data
Related structure data | 1hlgS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42933.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: LIPF / Plasmid: pUC18 / Production host: Zea mays (maize) / Strain (production host): Hi-II maize germplasm / References: UniProt: P80035, triacylglycerol lipase #2: Sugar | ChemComp-NAG / #3: Sugar | #4: Chemical | #5: 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: 2.6 Å3/Da / Density % sol: 52.61 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30 % PEGMME 2000, 0.1 M sodium acetate and 0.2 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
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: ESRF / Beamline: BM14 / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 27, 2000 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 25123 / Num. obs: 24343 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 2.7→2.75 Å / Rmerge(I) obs: 0.215 / % possible all: 88.7 |
Reflection | *PLUS Lowest resolution: 40 Å / Redundancy: 3 % |
Reflection shell | *PLUS % possible obs: 97.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HLG Resolution: 2.7→15 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refinement | *PLUS Lowest resolution: 15 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.192 / Rfactor Rfree: 0.258 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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