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Yorodumi- PDB-1ijl: Crystal structure of acidic phospholipase A2 from deinagkistrodon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ijl | ||||||
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Title | Crystal structure of acidic phospholipase A2 from deinagkistrodon acutus | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / THREE LONG HELIX / ONE TWO STRAND BETA SHEET / CALCIUM BINDING LOOP | ||||||
Function / homology | Function and homology information phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Deinagkistrodon acutus (Chinese moccasin) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Gu, L. / Zhang, H. / Song, S. / Zhou, Y. / Lin, Z. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of an acidic phospholipase A2 from the venom of Deinagkistrodon acutus. Authors: Gu, L. / Zhang, H. / Song, S. / Zhou, Y. / Lin, Z. #1: Journal: ACTA BIOCHIM.BIOPHYS.SINICA / Year: 1999 Title: Cloning and sequencing of gene encoding Phospholipase A2 from Agkistrodon Acutus Authors: Liu, X.L. / Pan, H. / Yang, G.Z. / Wu, X.F. / Zhou, Y.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ijl.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ijl.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ijl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ijl_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 1ijl_full_validation.pdf.gz | 436.2 KB | Display | |
Data in XML | 1ijl_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 1ijl_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/1ijl ftp://data.pdbj.org/pub/pdb/validation_reports/ij/1ijl | HTTPS FTP |
-Related structure data
Related structure data | 1psjS 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: 14091.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / References: UniProt: Q7SID6, phospholipase A2 #2: Chemical | ChemComp-ZN / | #3: Chemical | #4: 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: 2.26 Å3/Da / Density % sol: 45.67 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, sodium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 8966 / Num. obs: 8966 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.3 / Num. unique all: 898 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 80310 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PSJ Resolution: 2.6→8 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.184 / Rfactor Rfree: 0.225 | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å / Rfactor Rfree: 0.317 / Rfactor Rwork: 0.23 |