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- PDB-3o4m: Crystal structure of porcine pancreatic phospholipase A2 in compl... -

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Basic information

Entry
Database: PDB / ID: 3o4m
TitleCrystal structure of porcine pancreatic phospholipase A2 in complex with 1,2-dihydroxybenzene
ComponentsPhospholipase A2, major isoenzyme
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Catechol binding / PLA2 / Pancreatic Enzyme / Disulfide bond / Lipid degradation / Lipoprotein / Metal-binding / Palmitate / Pyrrolidone carboxylic acid / Pancreas / HYDROLASE-HYDROLASE INHIBITOR complex
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 / calcium-dependent phospholipase A2 activity ...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 / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / 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 / phospholipid binding / positive regulation of MAP kinase activity / cellular response to insulin stimulus / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / positive regulation of immune response / 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, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CATECHOL / 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: Chem.Biol.Drug Des. / Year: 2011
Title: Binding to PLA(2) may contribute to the anti-inflammatory activity of catechol
Authors: Dileep, K.V. / Tintu, I. / Mandal, P.K. / Karthe, P. / Haridas, M. / Sadasivan, C.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Database references / Structure summary

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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)14,2004
Polymers14,0101
Non-polymers1903
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.240, 69.240, 69.670
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

21A-527-

HOH

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Components

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


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-CAQ / CATECHOL / 1,2-DIHYDROXYBENZENE / Catechol


Mass: 110.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 64.26 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 5% MPD, 0.05M Tris Maleate, 5mM Calcium Chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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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: Apr 2, 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→59.96 Å / Num. all: 6960 / Num. obs: 6617 / % possible obs: 95.07 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.092
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.092 / Rsym value: 0.032 / % possible all: 95.07

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AutoMRmodel building
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
AutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.99 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.949 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 2.5 / σ(I): 2 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22257 326 4.7 %RANDOM
Rwork0.1816 ---
obs0.18355 6617 99.76 %-
all-979 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.261 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 10 56 1037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211008
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.9481366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5025123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.3332550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92815163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.195154
X-RAY DIFFRACTIONr_chiral_restr0.1260.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021787
X-RAY DIFFRACTIONr_mcbond_it0.9111.5619
X-RAY DIFFRACTIONr_mcangle_it1.7912993
X-RAY DIFFRACTIONr_scbond_it2.9333389
X-RAY DIFFRACTIONr_scangle_it4.834.5373
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 25 -
Rwork0.227 478 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 33.6615 Å / Origin y: -14.4358 Å / Origin z: 14.4289 Å
111213212223313233
T0.0963 Å20.0381 Å20.0031 Å2-0.1428 Å2-0.0286 Å2--0.0624 Å2
L1.2612 °2-0.8548 °2-0.5969 °2-7.7628 °22.078 °2--2.2229 °2
S0.1273 Å °0.1204 Å °-0.1655 Å °-0.2439 Å °-0.4066 Å °0.2809 Å °0.0827 Å °-0.1336 Å °0.2794 Å °

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