+Open data
-Basic information
Entry | Database: PDB / ID: 4qn9 | ||||||
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Title | Structure of human NAPE-PLD | ||||||
Components | N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D | ||||||
Keywords | HYDROLASE / PLD / NAPE / anandamide / bile acid / phospholipase / inflammation / pain / complex / NAE / AEA / OEA / PEA / MBL / PE / cannabinoid / fat / acyl / deoxycholate / obesity / phospholipid / membrane / steroid / drug / alpha-beta-beta-alpha fold / phosphodiesterase | ||||||
Function / homology | Function and homology information N-acetylphosphatidylethanolamine-hydrolysing phospholipase D / : / Biosynthesis of A2E, implicated in retinal degradation / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / membrane-bounded organelle / host-mediated regulation of intestinal microbiota composition / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipid catabolic process / bile acid binding ...N-acetylphosphatidylethanolamine-hydrolysing phospholipase D / : / Biosynthesis of A2E, implicated in retinal degradation / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / membrane-bounded organelle / host-mediated regulation of intestinal microbiota composition / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipid catabolic process / bile acid binding / retinoid metabolic process / photoreceptor outer segment membrane / temperature homeostasis / positive regulation of brown fat cell differentiation / positive regulation of inflammatory response / nuclear envelope / early endosome membrane / early endosome / Golgi membrane / Golgi apparatus / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.652 Å | ||||||
Authors | Garau, G. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Structure of human N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: regulation of fatty acid ethanolamide biosynthesis by bile acids. Authors: Magotti, P. / Bauer, I. / Igarashi, M. / Babagoli, M. / Marotta, R. / Piomelli, D. / Garau, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qn9.cif.gz | 310.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qn9.ent.gz | 257.3 KB | Display | PDB format |
PDBx/mmJSON format | 4qn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qn9_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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Full document | 4qn9_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 4qn9_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 4qn9_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/4qn9 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/4qn9 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45654.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C7orf18, NAPEPLD / Production host: Escherichia coli (E. coli) References: UniProt: Q6IQ20, N-acetylphosphatidylethanolamine-hydrolysing phospholipase D |
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-Non-polymers , 5 types, 118 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-DXC / ( #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 3.17 Å3/Da / Density % sol: 61.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.9 M lithium sulfate, 0.1 M HEPES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.652→82.358 Å / Num. all: 35852 / Num. obs: 35841 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.1 % / Biso Wilson estimate: 72.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.652→2.72 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.652→82.358 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.917 / SU B: 19.409 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.284 / 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: 75.844 Å2
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Refinement step | Cycle: LAST / Resolution: 2.652→82.358 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 5559 / Type: TIGHT THERMAL / Rms dev position: 3.54 Å / Weight position: 0.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.652→2.721 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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