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- PDB-5wzu: Crystal structure of human secreted phospholipase A2 group IIE wi... -

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Basic information

Entry
Database: PDB / ID: 5wzu
TitleCrystal structure of human secreted phospholipase A2 group IIE with Compound 24
ComponentsGroup IIE secretory phospholipase A2
KeywordsHYDROLASE/INHIBITOR / phospholipase A2 / 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 / phospholipase A2 activity / phosphatidylcholine metabolic process / phospholipase A2 ...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 / phospholipase A2 activity / phosphatidylcholine metabolic process / phospholipase A2 / low-density lipoprotein particle remodeling / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / phospholipid metabolic process / phospholipid binding / inflammatory response / calcium ion binding / extracellular region / cytoplasm
Similarity search - Function
Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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: 2.2 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 A2 group IIE
Authors: Hou, S. / Xu, T. / Xu, J. / Qu, L. / Xu, Y. / Chen, L. / Liu, J.
History
DepositionJan 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)14,7027
Polymers13,9861
Non-polymers7166
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.627, 60.469, 63.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2122

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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: 13986.137 Da / Num. of mol.: 1 / Fragment: UNP residues 20-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G2E / Plasmid: pGAPZaA / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q9NZK7, phospholipase A2

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Non-polymers , 6 types, 97 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.34 Å3/Da / Density % sol: 63.15 % / Mosaicity: 0.99 °
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: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5406 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Sep 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.2→18.48 Å / Num. obs: 9973 / % possible obs: 99.8 % / Redundancy: 9.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.032 / Rrim(I) all: 0.102 / Net I/σ(I): 20.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.412 / CC1/2: 0.956 / Rpim(I) all: 0.14 / Rrim(I) all: 0.436 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WZM

5wzm


Resolution: 2.2→18.48 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 4.674 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.183
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 473 4.7 %RANDOM
Rwork0.1954 ---
obs0.1974 9489 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.34 Å2 / Biso mean: 29.379 Å2 / Biso min: 6.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2--1.47 Å2-0 Å2
3----1.42 Å2
Refinement stepCycle: final / Resolution: 2.2→18.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 44 91 1106
Biso mean--56.67 27.98 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021069
X-RAY DIFFRACTIONr_bond_other_d0.0030.02964
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9911452
X-RAY DIFFRACTIONr_angle_other_deg1.0293.0062220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8522.24549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42915174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4781510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211206
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02268
LS refinement shellResolution: 2.2→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 33 -
Rwork0.211 671 -
all-704 -
obs--99.86 %

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