+Open data
-Basic information
Entry | Database: PDB / ID: 6kqu | ||||||
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Title | Crystal structure of phospholipase A2 | ||||||
Components | Group IIE secretory phospholipase A2 | ||||||
Keywords | HYDROLASE / phospholipase A2 / Mutation / calcium | ||||||
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 Å | ||||||
Authors | Hou, S. / Xu, T. / Liu, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochimie / Year: 2020 Title: Residue Asn21 acts as a switch for calcium binding to modulate the enzymatic activity of human phospholipase A2 group IIE. Authors: Hou, S. / Zhang, Y. / Xu, J. / Bai, J. / Liu, J. / Xie, J. / Xu, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kqu.cif.gz | 46.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kqu.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 6kqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/6kqu ftp://data.pdbj.org/pub/pdb/validation_reports/kq/6kqu | HTTPS FTP |
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-Related structure data
Related structure data | 5wzmS 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: 13929.085 Da / Num. of mol.: 1 / Mutation: N21G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G2E / Plasmid: pGAPZaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q9NZK7, phospholipase A2 |
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-Non-polymers , 6 types, 161 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-B3P / | #7: Water | ChemComp-HOH / | |
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-Details
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: 3.45 Å3/Da / Density % sol: 64.38 % / Mosaicity: 0.85 ° |
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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: 277 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: Jun 11, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→18.8 Å / Num. obs: 13357 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.043 / Rrim(I) all: 0.149 / Net I/σ(I): 21.1 / Num. measured all: 148885 / Scaling rejects: 284 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WZM Resolution: 2→18.8 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 3.356 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.148 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: 61.78 Å2 / Biso mean: 17.841 Å2 / Biso min: 5.86 Å2
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Refinement step | Cycle: final / Resolution: 2→18.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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