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- PDB-1jia: STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jia | ||||||
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Title | STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS AT 2.13A RESOLUTION | ||||||
![]() | PHOSPHOLIPASE A2 | ||||||
![]() | PHOSPHOLIPASE / PHOSPHOLIPASE A2 / AGKISTRODON HALYS PALLAS CRYSTAL STRUCTURE | ||||||
Function / homology | ![]() calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / toxin activity / signaling receptor binding ...calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / toxin activity / signaling receptor binding / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Zhao, K. / Lin, Z. | ||||||
![]() | ![]() Title: Structure of a basic phospholipase A2 from Agkistrodon halys Pallas at 2.13 A resolution. Authors: Zhao, K. / Song, S. / Lin, Z. / Zhou, Y. #1: ![]() Title: Preliminary Crystallographic Studies of a Basic Phospholipase A2 from the Venom of Agkistrodon Halys Pallas Authors: Zhao, K. / Song, S. / Lin, Z. / Zhou, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.2 KB | Display | ![]() |
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PDB format | ![]() | 47.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 431.7 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.10143, -0.99475, -0.01393), Vector: |
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Components
#1: Protein | Mass: 13923.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 37 % Description: THE STRUCTURE OF BASIC PLA2 FROM AGKISTRODON HALYS PALLAS WAS DETERMINED BY MOLECULAR REPLACEMENT METHOD, USING R CHAIN OF PLA2 FROM THE VENOM OF WESTERN DIAMONDBACK RATTLESNAKE(2.5A) AS A SEARCH MODEL. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9.5 Details: THE PROTEIN SOLUTIONS CONTAINED 10MM CA2+, 0.1M NACL, 5% PEG 4K IN 0.01M CHESS BUFFER (PH 9.5) AND AN ENZYME CONCENTRATION OF 11MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 10% PEG 4K IN SAME ...Details: THE PROTEIN SOLUTIONS CONTAINED 10MM CA2+, 0.1M NACL, 5% PEG 4K IN 0.01M CHESS BUFFER (PH 9.5) AND AN ENZYME CONCENTRATION OF 11MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 10% PEG 4K IN SAME BUFFER, ROOM TEMPERATURE OF 17 DEGREES C. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS-NICOLET X200B / Detector: AREA DETECTOR / Date: May 1, 1995 |
Radiation | Monochromator: NICKEL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→40 Å / Num. obs: 12001 / % possible obs: 86.1 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 26.24 Å2 / Rmerge(I) obs: 0.0459 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 2.13→2.23 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.9 / % possible all: 46.28 |
Reflection | *PLUS Num. measured all: 29753 |
Reflection shell | *PLUS % possible obs: 46.28 % |
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Processing
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Refinement | Method to determine structure: STRUCTURE REFINEMENT / Resolution: 2.13→6 Å Cross valid method: FULL REFINEMENT CONSISTING OF INITIAL MINIMIZATION, SLOW COOLING-SA 3000K, POSITIONAL AND B-FACTOR REFINEMENT. σ(F): 3 Details: DURING THE REFINEMENT, NO NCS RESTRAINTS WERE USED.
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Displacement parameters | Biso mean: 25.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.22 Å / Total num. of bins used: 1
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.242 |