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

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Basic information

Entry
Database: PDB / ID: 5wzt
TitleCrystal structure of human secreted phospholipase A2 group IIE with Compound 14
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-7W6 / Group IIE secretory phospholipase A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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)14,6425
Polymers13,9861
Non-polymers6564
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.930, 60.676, 63.379
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 , 5 types, 54 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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-7W6 / 2-[1-[(3-bromophenyl)methyl]-2-methyl-3-oxamoyl-indol-4-yl]oxyethanoic acid


Mass: 445.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17BrN2O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.36 Å3/Da / Density % sol: 63.43 % / Mosaicity: 1.21 °
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 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.4→18.47 Å / Num. obs: 7799 / % possible obs: 99.8 % / Redundancy: 9.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.042 / Rrim(I) all: 0.13 / Net I/σ(I): 16.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.604 / CC1/2: 0.889 / Rpim(I) all: 0.196 / Rrim(I) all: 0.636 / % 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: 2.4→18.47 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.861 / SU B: 6.977 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.248
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 373 4.8 %RANDOM
Rwork0.2186 ---
obs0.221 7405 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.75 Å2 / Biso mean: 32.773 Å2 / Biso min: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--3.04 Å2-0 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 2.4→18.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 39 50 1060
Biso mean--49.96 27.44 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191050
X-RAY DIFFRACTIONr_bond_other_d0.0020.02945
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.991422
X-RAY DIFFRACTIONr_angle_other_deg0.9443.0062176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.385124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10822.3447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14215169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.653159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02260
LS refinement shellResolution: 2.4→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 21 -
Rwork0.269 534 -
all-555 -
obs--99.82 %

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