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- PDB-1p2p: STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 AT 2.6 ANGSTROMS... -

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Basic information

Entry
Database: PDB / ID: 1p2p
TitleSTRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 AT 2.6 ANGSTROMS RESOLUTION AND COMPARISON WITH BOVINE PHOSPHOLIPASE A2
ComponentsPHOSPHOLIPASE A2
KeywordsCARBOXYLIC ESTER HYDROLASE
Function / homology
Function and homology information


regulation of D-glucose import / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / bile acid binding / phospholipase A2 / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity ...regulation of D-glucose import / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / bile acid binding / phospholipase A2 / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / positive regulation of immune response / phospholipid binding / cellular response to insulin stimulus / positive regulation of fibroblast proliferation / fatty acid biosynthetic process / positive regulation of MAPK cascade / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 / 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
Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsDijkstra, B.W. / Renetseder, R. / Kalk, K.H. / Hol, W.G.J. / Drenth, J.
Citation
Journal: J.Mol.Biol. / Year: 1983
Title: Structure of porcine pancreatic phospholipase A2 at 2.6 A resolution and comparison with bovine phospholipase A2.
Authors: Dijkstra, B.W. / Renetseder, R. / Kalk, K.H. / Hol, W.G. / Drenth, J.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: The Structure of Bovine Pancreatic Prophospholipase A2 at 3.0 Angstroms Resolution
Authors: Dijkstra, B.W. / Vannes, G.J.H. / Kalk, K.H. / Brandenburg, N.P. / Hol, W.G.J. / Drenth, J.
#2: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of Bovine Pancreatic Phospholipase A2 at 1.7 Angstroms Resolution
Authors: Dijkstra, B.W. / Kalk, K.H. / Hol, W.G.J. / Drenth, J.
#3: Journal: Nature / Year: 1981
Title: Active Site and Catalytic Mechanism of Phospholipase A2
Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H.
#4: Journal: J.Mol.Biol. / Year: 1978
Title: Three-Dimensional Structure and Disulfide Bond Connections in Bovine Pancreatic Phospholipase A2
Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H. / Vandermaelen, P.J.
History
DepositionJun 27, 1983Processing site: BNL
Revision 1.0Sep 15, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0903
Polymers14,0101
Non-polymers802
Water905
1
A: PHOSPHOLIPASE A2
hetero molecules

A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1806
Polymers28,0192
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+5/31
Buried area1560 Å2
ΔGint-49 kcal/mol
Surface area12980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.820, 69.820, 67.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: SEE REMARK 8. / 2: SEE REMARK 4.
Components on special symmetry positions
IDModelComponents
11A-126-

CA

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 14009.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE TYPE CLASSIFICATIONS GIVEN IN THE REMARK FIELD OF THE TURN RECORDS BELOW FOLLOWS THE ...THE TYPE CLASSIFICATIONS GIVEN IN THE REMARK FIELD OF THE TURN RECORDS BELOW FOLLOWS THE NOMENCLATURE OF CRAWFORD ET AL. (PROC.NAT.ACAD.SCI.USA, V. 76, P. 2551, 1973).
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.79 %
Crystal grow
*PLUS
pH: 7.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.05 MTris-maleate11
25 mM11CaCl2
3methanol110.010-0.015ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. all: 6144 / Num. obs: 4603 / % possible obs: 74.9 % / Rmerge(I) obs: 0.058

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor Rwork: 0.241 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 2 5 978
Refinement
*PLUS
Lowest resolution: 7 Å / Num. reflection obs: 4295 / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_plane_restr0.0025
X-RAY DIFFRACTIONo_chiral_restr0.086
X-RAY DIFFRACTIONo_mcbond_it2.01
X-RAY DIFFRACTIONo_scbond_it1.94
X-RAY DIFFRACTIONo_mcangle_it3.42
X-RAY DIFFRACTIONo_scangle_it3.28

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