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- PDB-2bp2: THE STRUCTURE OF BOVINE PANCREATIC PROPHOSPHOLIPASE A2 AT 3.0 ANG... -

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Entry
Database: PDB / ID: 2bp2
TitleTHE STRUCTURE OF BOVINE PANCREATIC PROPHOSPHOLIPASE A2 AT 3.0 ANGSTROMS RESOLUTION
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE ZYMOGEN
Function / homology
Function and homology information


Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / bile acid binding ...Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / bile acid binding / phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / innate immune response in mucosa / phospholipid binding / positive regulation of fibroblast proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / fatty acid biosynthetic process / antibacterial humoral response / defense response to Gram-positive bacterium / signaling receptor binding / calcium ion binding / cell surface / extracellular space
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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsDijkstra, B.W. / Vannes, G.J.H. / Kalk, K.H. / Brandenburg, N.P. / Hol, W.G.J. / Drenth, J.
Citation
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.
#1: 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.
#2: Journal: Nature / Year: 1981
Title: Active Site and Catalytic Mechanism of Phospholipase A2
Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H.
#3: Journal: Thesis / Year: 1980
Title: Structure and Mechanism of Phospholipase A2
Authors: Dijkstra, B.W.
#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.
History
DepositionJun 5, 1981Processing site: BNL
Revision 1.0Jul 16, 1981Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)14,5391
Polymers14,5391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.950, 46.950, 102.040
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 ABOVE.

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 14539.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00593
Compound detailsTHE ZYMOGEN PROPHOSPHOLIPASE A2 CONTAINS SEVEN EXTRA RESIDUES AT THE N-TERMINUS COMPARED WITH THE ...THE ZYMOGEN PROPHOSPHOLIPASE A2 CONTAINS SEVEN EXTRA RESIDUES AT THE N-TERMINUS COMPARED WITH THE ACTIVE ENZYME PHOSPHOLIPASE A2.
Has protein modificationY
Sequence detailsSEQUENCE NUMBERING IS THE SAME AS FOR THE ACTIVE ENZYME, I. E. THE FIRST RESIDUE IS NUMBERED -7.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal grow
*PLUS
pH: 7.6 / Method: unknown / Details: Dijkstra, B.W., (1978) J.Mol.Biol., 124, 53.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mMTris11
25 mM11CaCl2
330 mg/mlprotein11
4MPD120.05ml

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor Rwork: 0.219 / Highest resolution: 3 Å
Details: RESIDUES 1 TO 3 INCLUSIVE AND 62 TO 73 INCLUSIVE ARE VIRTUALLY INVISIBLE IN ELECTRON DENSITY MAPS AND ARE PROBABLY DISORDERED. THE COORDINATES GIVEN BELOW FOR THESE RESIDUES CONTAIN, ...Details: RESIDUES 1 TO 3 INCLUSIVE AND 62 TO 73 INCLUSIVE ARE VIRTUALLY INVISIBLE IN ELECTRON DENSITY MAPS AND ARE PROBABLY DISORDERED. THE COORDINATES GIVEN BELOW FOR THESE RESIDUES CONTAIN, THEREFORE, VERY LARGE ERRORS.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 0 0 956
Refinement
*PLUS
Lowest resolution: 7.1 Å / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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