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- PDB-4o1y: Crystal structure of Porcine Pancreatic Phospholipase A2 in compl... -

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Basic information

Entry
Database: PDB / ID: 4o1y
TitleCrystal structure of Porcine Pancreatic Phospholipase A2 in complex with 1-Naphthaleneacetic acid
ComponentsPhospholipase A2, major isoenzyme
KeywordsHYDROLASE / 1-Naphthaleneacetic acid binding / PLA2 / Pancreatic enzyme
Function / homology
Function and homology information


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 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
NAPHTHALEN-1-YL-ACETIC ACID / Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDileep, K.V. / Remya, C. / Tintu, I. / Mandal, P.K. / Karthe, P. / Haridas, M. / Sadasivan, C.
CitationJournal: To be published
Title: Crystal structure of Porcine Pancreatic Phospholipase A2 in complex with 1-Naphthaleneacetic acid
Authors: Dileep, K.V. / Remya, C. / Tintu, I. / Mandal, P.K. / Karthe, P. / Haridas, M. / Sadasivan, C.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

Deposited unit
A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2764
Polymers14,0101
Non-polymers2663
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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-335-

HOH

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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 / Details: Pancreas / Source: (natural) Sus scrofa (pig) / References: UniProt: P00592, phospholipase A2
#2: Chemical ChemComp-NLA / NAPHTHALEN-1-YL-ACETIC ACID


Mass: 186.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O2
#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


Mass: 18.015 Da / Num. of mol.: 38 / 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 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: Apr 14, 2011 / 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→12.92 Å / Num. obs: 6377 / % possible obs: 97.55 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.079 / Rsym value: 0.03 / Net I/σ(I): 16.9
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 0.03 / Num. unique all: 6377 / % possible all: 97.55

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P2P

1p2p


Resolution: 2.5→12.92 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 17.817 / SU ML: 0.206 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.5 / σ(I): 2 / ESU R: 0.32 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24518 317 4.7 %RANDOM
Rwork0.18519 ---
all0.273 ---
obs0.18791 6377 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.518 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→12.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 16 38 1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021015
X-RAY DIFFRACTIONr_angle_refined_deg1.871.9561376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0235123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.2232550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.24815163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.293154
X-RAY DIFFRACTIONr_chiral_restr0.1240.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021794
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 14 -
Rwork0.272 406 -
obs--96.77 %
Refinement TLS params.Method: refined / Origin x: -35.3623 Å / Origin y: 14.222 Å / Origin z: -2.6052 Å
111213212223313233
T0.1487 Å2-0.1002 Å2-0.0131 Å2-0.2275 Å2-0.0437 Å2--0.1047 Å2
L1.2445 °20.4771 °20.3429 °2-7.9471 °22.0866 °2--1.6748 °2
S0.1749 Å °-0.1363 Å °0.0895 Å °0.422 Å °-0.5506 Å °0.2715 Å °-0.0901 Å °-0.1889 Å °0.3757 Å °

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