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Open data
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Basic information
Entry | Database: PDB / ID: 1le6 | ||||||
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Title | CARBOXYLIC ESTER HYDROLASE, P 1 21 1 SPACE GROUP | ||||||
![]() | Group X Secretory Phospholipase A2 | ||||||
![]() | HYDROLASE / Human Phosphatidylcholine 2-acylhydrolase GX / GX sPLA2 / sPLA2-X | ||||||
Function / homology | ![]() phosphatidylserine metabolic process / lysophospholipid transport / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / production of molecular mediator involved in inflammatory response / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC ...phosphatidylserine metabolic process / lysophospholipid transport / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / production of molecular mediator involved in inflammatory response / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / phospholipase activity / Acyl chain remodelling of PS / Acyl chain remodelling of PE / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Synthesis of PA / negative regulation of cholesterol efflux / phosphatidylglycerol metabolic process / arachidonic acid metabolic process / phosphatidylcholine catabolic process / phosphatidylcholine metabolic process / positive regulation of prostaglandin secretion / phospholipase A2 activity / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / macrophage activation / positive regulation of arachidonic acid secretion / low-density lipoprotein particle remodeling / fertilization / calcium-dependent phospholipase A2 activity / phospholipase A2 / prostaglandin biosynthetic process / regulation of macrophage activation / arachidonic acid secretion / hair follicle morphogenesis / erythrocyte maturation / negative regulation of cytokine production involved in inflammatory response / phospholipid metabolic process / positive regulation of protein metabolic process / acrosomal vesicle / cellular response to leukemia inhibitory factor / cholesterol homeostasis / axon guidance / negative regulation of DNA-binding transcription factor activity / phospholipid binding / negative regulation of inflammatory response / defense response to virus / lysosome / calcium ion binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pan, Y.H. / Jain, M.K. / Bahnson, B.J. | ||||||
![]() | ![]() Title: Crystal structure of human group X secreted phospholipase A2. Electrostatically neutral interfacial surface targets zwitterionic membranes. Authors: Pan, Y.H. / Yu, B.Z. / Singer, A.G. / Ghomashchi, F. / Lambeau, G. / Gelb, M.H. / Jain, M.K. / Bahnson, B.J. | ||||||
History |
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Remark 600 | HETEROGEN In subunit A, HOH 1 is the N-terminal associated water, 5 and 12 are calcium coordinated ...HETEROGEN In subunit A, HOH 1 is the N-terminal associated water, 5 and 12 are calcium coordinated waters, 6 is the putative catalytic assisted water. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.5 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.4 KB | Display | ![]() |
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Full document | ![]() | 461.3 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1le7C ![]() 1pobS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13644.535 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.36 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: PEG3500, MPD, ETHYLENE GLYCOL, CALCIUM CHLORIDE, HEPES BUFFER, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 7, 2001 / Details: MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→28.36 Å / Num. all: 34475 / Num. obs: 34412 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 3399 / % possible all: 99.6 |
Reflection | *PLUS Num. obs: 34475 / Num. measured all: 337721 / Rmerge(I) obs: 0.063 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1POB Resolution: 1.97→28.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 413862.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.3513 Å2 / ksol: 0.342686 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.97→28.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.09 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 6 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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