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- PDB-3qlm: Crystal structure of porcine pancreatic phospholipase A2 in compl... -

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Basic information

Entry
Database: PDB / ID: 3qlm
TitleCrystal structure of porcine pancreatic phospholipase A2 in complex with n-hexadecanoic acid
ComponentsPhospholipase A2, major isoenzyme
KeywordsHYDROLASE / Pla2 / Pancreatic enzyme / palmitic acid binding
Function / homology
Function and homology information


positive regulation of podocyte apoptotic process / regulation of D-glucose import / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / calcium-dependent phospholipase A2 activity ...positive regulation of podocyte apoptotic process / regulation of D-glucose import / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / calcium-dependent phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / phospholipid metabolic process / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / positive regulation of MAP kinase activity / phospholipid binding / cellular response to insulin stimulus / fatty acid biosynthetic process / positive regulation of immune response / positive regulation of fibroblast proliferation / positive regulation of NF-kappaB transcription factor activity / intracellular signal transduction / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / 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, aspartic acid active site / Phospholipase A2 aspartic acid active site. / 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
PALMITIC ACID / Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAparna, V. / Dileep, K.V. / Karthe, P. / Mandal, P.K. / Sadasivan, C. / Haridas, M.
CitationJournal: Chem.Biol.Drug Des. / Year: 2012
Title: Anti-inflammatory property of n-hexadecanoic acid: Structural evidence and Kinetic assessment.
Authors: Aparna, V. / Dileep, K.V. / Mandal, P.K. / Karthe, P. / Sadasivan, C. / Haridas, M.
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3464
Polymers14,0101
Non-polymers3373
Water1,04558
1
A: Phospholipase A2, major isoenzyme
hetero molecules

A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6938
Polymers28,0192
Non-polymers6736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area1230 Å2
ΔGint-7 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.260, 69.260, 69.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-125-

CA

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Components

#1: Protein Phospholipase A2, major isoenzyme / Group IB phospholipase A2 / Phosphatidylcholine 2-acylhydrolase 1B


Mass: 14009.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: Pancreas / References: UniProt: P00592, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 64.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 15% MPD, 0.05M Tris Maliate, 5mM Calcium Chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2010 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.5→45.44 Å / Num. all: 6866 / Num. obs: 6010 / % possible obs: 90.4 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.079 / Rsym value: 0.084
Reflection shellResolution: 2.6→2.74 Å / % possible all: 90.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O4M

3o4m


Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.089 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24935 295 4.7 %RANDOM
Rwork0.19137 ---
obs0.19411 5654 91.13 %-
all-6866 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.616 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 20 58 1049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221017
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.951373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.625123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.9182550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.13115163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.11154
X-RAY DIFFRACTIONr_chiral_restr0.1320.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021783
X-RAY DIFFRACTIONr_mcbond_it1.0481.5619
X-RAY DIFFRACTIONr_mcangle_it2.0622993
X-RAY DIFFRACTIONr_scbond_it2.9063398
X-RAY DIFFRACTIONr_scangle_it5.0234.5380
LS refinement shellResolution: 2.502→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 25 -
Rwork0.25 468 -
obs--100 %

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