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

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Basic information

Entry
Database: PDB / ID: 5wzv
TitleCrystal structure of human secreted phospholipase A2 group IIE with Me-indoxam
ComponentsGroup IIE secretory phospholipase A2
KeywordsHYDROLASE/INHIBITOR / phospholipase A2 / inhibitor / 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-7W0 / 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 2.0Nov 22, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group IIE secretory phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8028
Polymers13,9861
Non-polymers8167
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.076, 61.048, 63.328
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-337-

HOH

21A-382-

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: 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, 109 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-7W0 / 2-[2-methyl-3-oxamoyl-1-[(2-phenylphenyl)methyl]indol-4-yl]oxyethanoic acid


Mass: 442.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H22N2O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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.: 102 / 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: 3.39 Å3/Da / Density % sol: 63.73 % / Mosaicity: 1.17 °
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 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.2→19.37 Å / Num. obs: 10042 / % possible obs: 99.2 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.051 / Rrim(I) all: 0.139 / Net I/σ(I): 13.9 / Num. measured all: 71369 / Scaling rejects: 118
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.674 / CC1/2: 0.823 / Rpim(I) all: 0.258 / Rrim(I) all: 0.723 / % possible all: 99.9

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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→19.37 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / SU B: 5.501 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.186
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 472 4.7 %RANDOM
Rwork0.2082 ---
obs0.2097 9553 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.39 Å2 / Biso mean: 30.496 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--1.06 Å2-0 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 2.2→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 52 102 1125
Biso mean--55.01 30.65 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191068
X-RAY DIFFRACTIONr_bond_other_d0.0030.02963
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9991446
X-RAY DIFFRACTIONr_angle_other_deg1.0313.0072217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7585126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9422.548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88815171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.02159
X-RAY DIFFRACTIONr_chiral_restr0.080.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
LS refinement shellResolution: 2.2→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 33 -
Rwork0.263 694 -
all-727 -
obs--99.73 %

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