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Yorodumi- PDB-5izr: Human GIVD cytosolic phospholipase A2 in complex with Methyl gamm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5izr | ||||||
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Title | Human GIVD cytosolic phospholipase A2 in complex with Methyl gamma-Linolenyl Fluorophosphonate inhibitor and Terbium Chloride | ||||||
Components | Cytosolic phospholipase A2 delta | ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / Signal Transduction / phospholipase / inhibitor / HYDROLASE-HYDROLASE inhibitor complex | ||||||
Function / homology | Function and homology information phosphatidylglycerol acyl-chain remodeling / phosphatidylinositol acyl-chain remodeling / glycerophospholipid catabolic process / Hydrolysis of LPC / Acyl chain remodelling of PG / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE ...phosphatidylglycerol acyl-chain remodeling / phosphatidylinositol acyl-chain remodeling / glycerophospholipid catabolic process / Hydrolysis of LPC / Acyl chain remodelling of PG / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / calcium-dependent phospholipase A2 activity / calcium-dependent phospholipid binding / phospholipase A2 / fatty acid metabolic process / calcium ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 Å | ||||||
Authors | Wang, H. / Klein, M.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Structure of Human GIVD Cytosolic Phospholipase A2 Reveals Insights into Substrate Recognition. Authors: Wang, H. / Klein, M.G. / Snell, G. / Lane, W. / Zou, H. / Levin, I. / Li, K. / Sang, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5izr.cif.gz | 531.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5izr.ent.gz | 446.8 KB | Display | PDB format |
PDBx/mmJSON format | 5izr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/5izr ftp://data.pdbj.org/pub/pdb/validation_reports/iz/5izr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 91444.305 Da / Num. of mol.: 4 / Fragment: UNP residues 2-810 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G4D / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86XP0, phospholipase A2 #2: Chemical | ChemComp-7FA / #3: Chemical | ChemComp-TB / #4: 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: 2.47 Å3/Da / Density % sol: 50.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM MES (pH 6.0-6.2), 10-14% (v/v) PEG20K and 50 mM sodium acetate PH range: 6.0-6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.65 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.65 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→159.2 Å / Num. obs: 56076 / % possible obs: 99.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 3.25→3.34 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.2 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 3.25→159.2 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.887 / SU B: 33.21 / SU ML: 0.511 / Cross valid method: THROUGHOUT / ESU R Free: 0.56 / 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: 85.699 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→159.2 Å
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Refine LS restraints |
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