[English] 日本語
Yorodumi- PDB-2ze4: Crystal structure of phospholipase D from streptomyces antibioticus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ze4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of phospholipase D from streptomyces antibioticus | ||||||
Components | Phospholipase D | ||||||
Keywords | HYDROLASE / alpha-beta-beta-alpha-sandwich / Lipid degradation / Secreted | ||||||
Function / homology | Function and homology information phosphatidyltransferase activity / cardiolipin biosynthetic process / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D / phospholipase D activity / lipid catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces antibioticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Suzuki, A. / Kakuno, K. / Saito, R. / Iwasaki, Y. / Yamane, T. / Yamane, T. | ||||||
Citation | Journal: To be Published 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ze4.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ze4.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ze4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/2ze4 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/2ze4 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 54036.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Plasmid: pPELB-PLD3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53728, phospholipase D |
---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.5→64.55 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.979 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.239 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→64.55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
|