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- PDB-2ddr: Crystal structure of sphingomyelinase from Bacillus cereus with c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ddr | ||||||
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Title | Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion | ||||||
![]() | Sphingomyelin phosphodiesterase | ||||||
![]() | HYDROLASE / DNase I like folding / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | ![]() sphingomyelin metabolic process / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / killing of cells of another organism / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ago, H. / Oda, M. / Takahashi, M. / Tsuge, H. / Ochi, S. / Katunuma, N. / Miyano, M. / Sakurai, J. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase from Bacillus cereus. Authors: Ago, H. / Oda, M. / Takahashi, M. / Tsuge, H. / Ochi, S. / Katunuma, N. / Miyano, M. / Sakurai, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 264.2 KB | Display | ![]() |
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PDB format | ![]() | 218.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.4 KB | Display | ![]() |
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Full document | ![]() | 470.6 KB | Display | |
Data in XML | ![]() | 56.1 KB | Display | |
Data in CIF | ![]() | 83.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34343.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P11889, sphingomyelin phosphodiesterase #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.59 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion / pH: 6.5 Details: 18% (w/v) PEG 8000, 0.2M calcium chloride, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 213905 / Num. obs: 213905 / % possible obs: 93.5 % / Biso Wilson estimate: 16.3 Å2 |
Reflection shell | Resolution: 1.4→1.48 Å / % possible all: 92.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.0713 Å2 / ksol: 0.316693 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→19.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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