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- PDB-1m8s: Crystal Structures of Cadmium-binding Acidic Phospholipase A2 fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m8s | ||||||
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Title | Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of Agkistrodon halys pallas at 1.9 Resolution (crystal grown at pH 5.9) | ||||||
![]() | phospholipase a2 | ||||||
![]() | HYDROLASE / phopholipase a2-metal cation complex / three alpha / two beta | ||||||
Function / homology | ![]() calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Xu, S. / Gu, L. / Zhou, Y. / Lin, Z. | ||||||
![]() | ![]() Title: Structures of cadmium-binding acidic phospholipase A(2) from the venom of Agkistrodon halys Pallas at 1.9A resolutio Authors: Xu, S. / Gu, L. / Jiang, T. / Zhou, Y. / Lin, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.2 KB | Display | ![]() |
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PDB format | ![]() | 27.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1m8rC ![]() 1psjS S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 13956.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P14418, UniProt: O42191*PLUS, phospholipase A2 | ||
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#2: Chemical | ChemComp-CD / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.52 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 10%(v/v) 1,4-butyldiol, 0.01M CdCl2, 0.1M Na(CH3)2AsO, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 11, 2001 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 10431 / Num. obs: 10431 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 9.7 / Num. unique all: 1024 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 25 Å / % possible obs: 100 % / Num. measured all: 187637 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.26 |
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Processing
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Refinement | Method to determine structure: isomorphous difference Fourier Starting model: PDB ENTRY 1PSJ Resolution: 1.9→25 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 126.972 Å2 / ksol: 0.44155 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.08 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.198 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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