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- PDB-2ze4: Crystal structure of phospholipase D from streptomyces antibioticus -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ze4 | ||||||
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Title | Crystal structure of phospholipase D from streptomyces antibioticus | ||||||
![]() | Phospholipase D | ||||||
![]() | HYDROLASE / alpha-beta-beta-alpha-sandwich / Lipid degradation / Secreted | ||||||
Function / homology | ![]() cardiolipin synthase activity / cardiolipin biosynthetic process / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D activity / phospholipase D / lipid catabolic process / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, A. / Kakuno, K. / Saito, R. / Iwasaki, Y. / Yamane, T. / Yamane, T. | ||||||
![]() | ![]() Title: Crystal structure of phospholipase D from streptomyces antibioticus Authors: Suzuki, A. / Kakuno, K. / Saito, R. / Iwasaki, Y. / Yamane, T. / Yamane, T. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and preliminary X-ray diffraction studies of phospholipase D from Streptomyces antibioticus Authors: Suzuki, A. / Kakuno, K. / Iwasaki, Y. / Yamane, T. / Yamane, T. #2: Journal: Chembiochem / Year: 2008 Title: Streptomyces phospholipase D mutants with altered substrate specificity capable of phosphatidylinositol synthesis Authors: Masayama, A. / Takahashi, T. / Tsukada, K. / Nishikawa, S. / Takahashi, R. / Adachi, M. / Koga, K. / Suzuki, A. / Yamane, T. / Nakano, H. / Iwasaki, 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 | ![]() | 105.9 KB | Display | ![]() |
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PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 54036.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MES / |
#3: Water | ChemComp-HOH / |
Sequence details | THERE ARE DIFFERENCES BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. ACCORDING TO THE DEPOSITOR, THE ...THERE ARE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 15% PEG 6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Dec 8, 1997 / Details: mirrors |
Radiation | Monochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. all: 19350 / Num. obs: 17415 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.151 / % possible all: 78.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.338 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→64.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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