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Yorodumi- PDB-1clp: CRYSTAL STRUCTURE OF A CALCIUM-INDEPENDENT PHOSPHOLIPASELIKE MYOT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1clp | ||||||
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Title | CRYSTAL STRUCTURE OF A CALCIUM-INDEPENDENT PHOSPHOLIPASELIKE MYOTOXIC PROTEIN FROM BOTHROPS ASPER VENOM | ||||||
Components | MYOTOXIN II | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / heparin binding / toxin activity / defense response to bacterium / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Bothrops asper (terciopelo) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Arni, R.K. / Ward, R.J. / Gutierrez, J.M. / Tulinsky, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Structure of a calcium-independent phospholipase-like myotoxic protein from Bothrops asper venom. Authors: Arni, R.K. / Ward, R.J. / Gutierrez, J.M. / Tulinsky, A. #1: Journal: Toxicon / Year: 1993 Title: Crystallization and Preliminary Diffraction Data of Two Myotoxins Isolated from the Venoms of Bothrops Asper (Terciopelo) and Bothrops Nummifer (Jumping Viper) Authors: Arni, R.K. / Gutierrez, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1clp.cif.gz | 58.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1clp.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 1clp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/1clp ftp://data.pdbj.org/pub/pdb/validation_reports/cl/1clp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.3338, -0.0176, -0.9425), Vector: Details | MTRIX THE TRANSFORMATION PRESENTED ON MTRIX RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE *A* SUBUNIT WHEN APPLIED TO THE *B* SUBUNIT. | |
-Components
#1: Protein | Mass: 13764.138 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bothrops asper (terciopelo) / References: UniProt: P24605, phospholipase A2 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.72 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 4.6 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 23021 / Observed criterion σ(I): 3 |
Reflection | *PLUS Num. obs: 5805 / Num. measured all: 23021 / Rmerge(I) obs: 0.056 |
-Processing
Software |
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Refinement | Resolution: 2.8→7 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Resolution: 2.8→7 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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