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Yorodumi- PDB-4x93: Crystal structure of Lysosomal Phospholipase A2 crystallized in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x93 | ||||||
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Title | Crystal structure of Lysosomal Phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (tetragonal form) | ||||||
Components | Group XV phospholipase A2 | ||||||
Keywords | TRANSFERASE / hydrolase / phospholipase / esterase / acyltransferase | ||||||
Function / homology | Function and homology information acylglycerol O-acyltransferase activity / phosphatidylethanolamine catabolic process / Hydrolysis of LPC / phosphatidylserine metabolic process / phosphatidyl phospholipase B activity / lysophospholipase / glycerophospholipid metabolic process / phospholipase A1 / O-acyltransferase activity / phosphatidylserine 1-acylhydrolase activity ...acylglycerol O-acyltransferase activity / phosphatidylethanolamine catabolic process / Hydrolysis of LPC / phosphatidylserine metabolic process / phosphatidyl phospholipase B activity / lysophospholipase / glycerophospholipid metabolic process / phospholipase A1 / O-acyltransferase activity / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / calcium-independent phospholipase A2 activity / diacylglycerol biosynthetic process / phosphatidylglycerol metabolic process / ceramide metabolic process / phosphatidylcholine catabolic process / fatty acid catabolic process / phosphatidylcholine metabolic process / lysophospholipase activity / phospholipase A2 / phospholipid metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / phospholipid binding / lysosome / intracellular membrane-bounded organelle / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Glukhova, A. / Tesmer, J.J.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2015 Title: Structure and function of lysosomal phospholipase A2 and lecithin:cholesterol acyltransferase. Authors: Glukhova, A. / Hinkovska-Galcheva, V. / Kelly, R. / Abe, A. / Shayman, J.A. / Tesmer, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x93.cif.gz | 326.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x93.ent.gz | 268.8 KB | Display | PDB format |
PDBx/mmJSON format | 4x93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x93_validation.pdf.gz | 681.1 KB | Display | wwPDB validaton report |
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Full document | 4x93_full_validation.pdf.gz | 688.9 KB | Display | |
Data in XML | 4x93_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 4x93_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/4x93 ftp://data.pdbj.org/pub/pdb/validation_reports/x9/4x93 | HTTPS FTP |
-Related structure data
Related structure data | 4x90SC 4x91C 4x92C 4x94C 4x95C 4x96C 4x97C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 4 - 378 / Label seq-ID: 5 - 379
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-Components
-Protein / Sugars , 2 types, 10 molecules AB
#1: Protein | Mass: 43121.027 Da / Num. of mol.: 2 / Fragment: UNP residues 34-412 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G15, LYPLA3, UNQ341/PRO540 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) References: UniProt: Q8NCC3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 95 molecules
#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-PE8 / | #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: 4.01 Å3/Da / Density % sol: 69.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5, 30% PEG MME 550, 50 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97933 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→30 Å / Num. obs: 44707 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.049 / Rrim(I) all: 0.165 / Χ2: 1.508 / Net I/av σ(I): 23.545 / Net I/σ(I): 4.4 / Num. measured all: 654390 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X90 Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 17.517 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 152.93 Å2 / Biso mean: 62.707 Å2 / Biso min: 32.14 Å2
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Refinement step | Cycle: final / Resolution: 2.6→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 23361 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.6→2.667 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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