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- PDB-5wzm: Crystal structure of human secreted phospholipase A2 group IIE -

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Basic information

Entry
Database: PDB / ID: 5wzm
TitleCrystal structure of human secreted phospholipase A2 group IIE
ComponentsGroup IIE secretory phospholipase A2
KeywordsHYDROLASE/INHIBITOR / 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
Group IIE secretory phospholipase A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 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 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)14,36713
Polymers13,7591
Non-polymers60812
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.510, 60.460, 63.590
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-335-

HOH

21A-403-

HOH

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Components

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


Mass: 13758.875 Da / Num. of mol.: 1 / Fragment: UNP residues 22-142
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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
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: 63.7 %
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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→43.82 Å / Num. obs: 13175 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.045 / Rrim(I) all: 0.12 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.06 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.601 / CC1/2: 0.836 / Rpim(I) all: 0.239 / Rrim(I) all: 0.648 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
MOLREPmodel building
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.82 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.372 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.136
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 647 4.9 %RANDOM
Rwork0.1847 ---
obs0.1867 12500 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.09 Å2 / Biso mean: 28.801 Å2 / Biso min: 14.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.65 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 2→43.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 26 105 1086
Biso mean--40.08 35.84 -
Num. residues----121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191010
X-RAY DIFFRACTIONr_bond_other_d0.0020.02920
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9641367
X-RAY DIFFRACTIONr_angle_other_deg1.04632123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23222.17446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8415166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.739159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 60 -
Rwork0.238 880 -
all-940 -
obs--100 %

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