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Yorodumi- PDB-8yk5: Structure of glycerophosphoethanolamine ethanolaminephosphodieste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8yk5 | ||||||
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Title | Structure of glycerophosphoethanolamine ethanolaminephosphodiesterase from Streptomyces sanglieri | ||||||
Components | phospholipase C | ||||||
Keywords | HYDROLASE / phosphodiesterase / long flexible linker / novel C-terminal domain | ||||||
Function / homology | Function and homology information phospholipase C / phosphatidylcholine phospholipase C activity / lipid catabolic process Similarity search - Function | ||||||
Biological species | Streptomyces sanglieri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Murayama, K. / Sugimori, D. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2024 Title: Structure of a phosphodiesterase from Streptomyces sanglieri with a novel C-terminal domain. Authors: Murayama, K. / Hosaka, T. / Shirouzu, M. / Sugimori, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yk5.cif.gz | 283.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yk5.ent.gz | 225.6 KB | Display | PDB format |
PDBx/mmJSON format | 8yk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yk5_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8yk5_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8yk5_validation.xml.gz | 53.7 KB | Display | |
Data in CIF | 8yk5_validation.cif.gz | 78.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/8yk5 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/8yk5 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 73845.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sanglieri (bacteria) / Gene: gpe-ep / Production host: Escherichia coli (E. coli) / References: UniProt: A0A077KPD5, phospholipase C #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-tris propane buffer (pH 6.5), 30% PEG 3350, 0.2 M sodium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 108015 / % possible obs: 95.5 % / Redundancy: 3.6 % / Rpim(I) all: 0.071 / Rrim(I) all: 0.139 / Net I/σ(I): 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.252 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→40.252 Å
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Refine LS restraints |
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LS refinement shell |
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