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Yorodumi- PDB-5wzv: Crystal structure of human secreted phospholipase A2 group IIE wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wzv | |||||||||
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Title | Crystal structure of human secreted phospholipase A2 group IIE with Me-indoxam | |||||||||
Components | Group IIE secretory phospholipase A2 | |||||||||
Keywords | HYDROLASE/INHIBITOR / phospholipase A2 / inhibitor / HYDROLASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / calcium-dependent phospholipase A2 activity / low-density lipoprotein particle remodeling / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / inflammatory response / calcium ion binding / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Hou, S. / Xu, J. / Xu, T. / Liu, J. | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Structural basis for functional selectivity and ligand recognition revealed by crystal structures of human secreted phospholipase A2 group IIE Authors: Hou, S. / Xu, T. / Xu, J. / Qu, L. / Xu, Y. / Chen, L. / Liu, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wzv.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wzv.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/5wzv ftp://data.pdbj.org/pub/pdb/validation_reports/wz/5wzv | HTTPS FTP |
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-Related structure data
Related structure data | 5wzmSC 5wzoC 5wzsC 5wztC 5wzuC 5wzwC 5y5eC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13986.137 Da / Num. of mol.: 1 / Fragment: UNP residues 20-142 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G2E / Plasmid: pGAPZaA / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q9NZK7, phospholipase A2 |
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-Non-polymers , 6 types, 109 molecules
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | ChemComp-7W0 / | ||||||
#4: Chemical | #5: Chemical | ChemComp-DMS / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.73 % / Mosaicity: 1.17 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 2.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5406 Å |
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: Sep 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.37 Å / Num. obs: 10042 / % possible obs: 99.2 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.051 / Rrim(I) all: 0.139 / Net I/σ(I): 13.9 / Num. measured all: 71369 / Scaling rejects: 118 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.674 / CC1/2: 0.823 / Rpim(I) all: 0.258 / Rrim(I) all: 0.723 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WZM Resolution: 2.2→19.37 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / SU B: 5.501 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.186 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.39 Å2 / Biso mean: 30.496 Å2 / Biso min: 8.14 Å2
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Refinement step | Cycle: final / Resolution: 2.2→19.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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