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- PDB-3hsw: Crystal Structure of Porcine Pancreatic Phospholipase A2 in Compl... -

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Basic information

Entry
Database: PDB / ID: 3hsw
TitleCrystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with 2-methoxycyclohexa-2-5-diene-1,4-dione
ComponentsPhospholipase A2, major isoenzyme
KeywordsHYDROLASE / Curcumin binding / PLA2 / Pancreatic Enzyme / Disulfide bond / Lipid degradation / Lipoprotein / Metal-binding / Palmitate / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process ...Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / 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 / fatty acid biosynthetic process / cellular response to insulin stimulus / positive regulation of immune response / positive regulation of fibroblast proliferation / positive regulation of NF-kappaB transcription factor activity / intracellular signal transduction / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / 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
2-methoxycyclohexa-2,5-diene-1,4-dione / Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDileep, K.V. / Tintu, I. / Karthe, P. / Mandal, P.K. / Haridas, M. / Sadasivan, C.
CitationJournal: Frontiers in life sci. / Year: 2012
Title: Crystal structure of porcine pancreatic phospholipase A2 in complex with 2-methoxycyclohexa-2-5-diene-1,4-dione
Authors: Dileep, K.V. / Tintu, I. / Mandal, P.K. / Karthe, P. / Haridas, M. / Sadasivan, C.
History
DepositionJun 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2284
Polymers14,0101
Non-polymers2183
Water57632
1
A: Phospholipase A2, major isoenzyme
hetero molecules

A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4568
Polymers28,0192
Non-polymers4376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area1560 Å2
ΔGint-50 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.360, 68.360, 70.120
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-502-

CA

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Components

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


Mass: 14009.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Pancreas / Source: (natural) Sus scrofa (pig) / References: UniProt: P00592, phospholipase A2
#2: Chemical ChemComp-MCW / 2-methoxycyclohexa-2,5-diene-1,4-dione


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 15% MPD, 0.05M Tris Maleate, 5mM Calcium Chloride, pH7.2, 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: Mar 22, 2009 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.5→45.24 Å / Num. all: 6789 / Num. obs: 6759 / % possible obs: 97.3 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073 / Rsym value: 0.065 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.073 / Num. unique all: 955 / Rsym value: 0.065 / % possible all: 70.79

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AutoMRmodel building
REFMAC5.5.0072refinement
iMOSFLMdata reduction
SCALAdata scaling
AutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P2P

1p2p


Resolution: 2.5→13.65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 17.329 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2.5 / σ(I): 2 / ESU R: 0.333 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22883 349 5.2 %RANDOM
Rwork0.17965 ---
all0.2303 6811 --
obs0.18214 6356 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.783 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→13.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 12 32 1015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211010
X-RAY DIFFRACTIONr_angle_refined_deg2.0791.9511369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1375123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2952550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.79215163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.049154
X-RAY DIFFRACTIONr_chiral_restr0.1350.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021788
X-RAY DIFFRACTIONr_mcbond_it0.841.5619
X-RAY DIFFRACTIONr_mcangle_it1.6442993
X-RAY DIFFRACTIONr_scbond_it2.5453391
X-RAY DIFFRACTIONr_scangle_it4.2244.5376
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 27 -
Rwork0.282 438 -
obs--97.08 %
Refinement TLS params.Method: refined / Origin x: -35.291 Å / Origin y: 14.13 Å / Origin z: -2.717 Å
111213212223313233
T0.1635 Å2-0.0893 Å2-0.0062 Å2-0.2206 Å2-0.0362 Å2--0.1219 Å2
L1.4708 °21.205 °20.6102 °2-9.9967 °22.5009 °2--2.6842 °2
S0.2397 Å °-0.167 Å °0.2022 Å °0.3095 Å °-0.6234 Å °0.3245 Å °-0.175 Å °-0.2479 Å °0.3837 Å °

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