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- PDB-5y5e: Crystal structure of phospholipase A2 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 5y5e
TitleCrystal structure of phospholipase A2 with inhibitor
ComponentsGroup IIE secretory phospholipase A2
KeywordsHYDROLASE/INHIBITOR / mutant / 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
Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7W3 / Group IIE secretory phospholipase A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHou, S. / Xu, J. / Xu, T. / Liu, J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis for functional selectivity and ligand recognition revealed by crystal structures of human secreted phospholipase A2group IIE
Authors: Hou, S. / Xu, T. / Xu, J. / Qu, L. / Xu, Y. / Chen, L. / Liu, J.
History
DepositionAug 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Group IIE secretory phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,97811
Polymers13,9291
Non-polymers1,04910
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, This protein in solution is a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area7160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.726, 61.063, 63.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2122
Components on special symmetry positions
IDModelComponents
11A-392-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Group IIE secretory phospholipase A2 / sPLA2-IIE / Phosphatidylcholine 2-acylhydrolase 2E


Mass: 13929.085 Da / Num. of mol.: 1 / Fragment: UNP residues 20-142 / 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 , 7 types, 154 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-7W3 / 2-[2-methyl-3-oxamoyl-1-[[2-(trifluoromethyl)phenyl]methyl]indol-4-yl]oxyethanoic acid


Mass: 434.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17F3N2O5
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.24 % / Mosaicity: 0.71 °
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 2.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→18.78 Å / Num. obs: 18109 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.02 / Rrim(I) all: 0.064 / Net I/σ(I): 24.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.845.60.44810250.880.2070.49598.9
9-18.785.80.0251590.9980.0110.02789.3

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Processing

Software
NameVersionClassification
Aimless0.1.30data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
CrysalisProdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WZM

5wzm


Resolution: 1.8→18.78 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.341 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.108
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.225 913 5 %RANDOM
Rwork0.1926 ---
obs0.1942 17182 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.7 Å2 / Biso mean: 22.551 Å2 / Biso min: 9.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.26 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.8→18.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 63 144 1158
Biso mean--36.84 28.58 -
Num. residues----121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021064
X-RAY DIFFRACTIONr_bond_other_d0.0040.02949
X-RAY DIFFRACTIONr_angle_refined_deg1.6172.0081445
X-RAY DIFFRACTIONr_angle_other_deg1.0383.0062195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8495126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08222.3447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50315168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.79159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211190
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02259
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 65 -
Rwork0.228 1205 -
all-1270 -
obs--99.06 %

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