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- PDB-2ze9: Crystal structure of H168A mutant of phospholipase D from Strepto... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ze9 | ||||||
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Title | Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine | ||||||
![]() | Phospholipase D | ||||||
![]() | HYDROLASE / ALPHA-BETA-BETA-ALPHA SANDWICH / Lipid degradation / Secreted | ||||||
Function / homology | ![]() cardiolipin synthase activity / cardiolipin biosynthetic process / phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D activity / lipid catabolic process / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Suzuki, A. / Toda, H. / Iwasaki, Y. / Yamane, T. / Yamane, T. | ||||||
![]() | ![]() Title: Crystal structure of phospholipase D from streptomyces antibioticus Authors: Suzuki, A. / Toda, H. / 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 | ![]() | 118.2 KB | Display | ![]() |
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PDB format | ![]() | 88.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 712.9 KB | Display | ![]() |
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Full document | ![]() | 721.9 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ze4SC 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: 53968.992 Da / Num. of mol.: 1 / Mutation: H168A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MES / |
#3: Chemical | ChemComp-PD7 / ( |
#4: 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: 2.17 Å3/Da / Density % sol: 43.45 % |
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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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 1999 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→61.31 Å / Num. all: 21448 / Num. obs: 20805 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2726 / % possible all: 88.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZE4 Resolution: 2.3→48.04 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.879 / SU B: 6.9 / SU ML: 0.17 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.481 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 13.618 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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