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- PDB-3bp2: ROLE OF THE N-TERMINUS IN THE INTERACTION OF PANCREATIC PHOSPHOLI... -

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Basic information

Entry
Database: PDB / ID: 3bp2
TitleROLE OF THE N-TERMINUS IN THE INTERACTION OF PANCREATIC PHOSPHOLIPASE A2 WITH AGGREGATED SUBSTRATES. PROPERTIES AND CRYSTAL STRUCTURE OF TRANSAMINATED PHOSPHOLIPASE A2
ComponentsPHOSPHOLIPASE A2
KeywordsCARBOXYLIC ESTER HYDROLASE
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 / calcium-dependent phospholipase A2 activity ...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 / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / innate immune response in mucosa / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / 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, 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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsDijkstra, B.W. / Drenth, J.
Citation
Journal: Biochemistry / Year: 1984
Title: Role of the N-terminus in the interaction of pancreatic phospholipase A2 with aggregated substrates. Properties and crystal structure of transaminated phospholipase A2
Authors: Dijkstra, B.W. / Kalk, K.H. / Drenth, J. / de Haas, G.H. / Egmond, M.R. / Slotboom, A.J.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Porcine Pancreatic Phospholipase A2 at 2.6 Angstroms Resolution and Comparison with Bovine Phospholipase A2
Authors: Dijkstra, B.W. / Renetseder, R. / Kalk, K.H. / Hol, W.G.J. / Drenth, J.
#2: 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.
#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: 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.
#5: 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 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2019Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8502
Polymers13,8091
Non-polymers401
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.680, 64.850, 37.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SEE REMARK 5.

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Components

#1: Protein PHOSPHOLIPASE A2 /


Mass: 13809.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00593, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal grow
*PLUS
pH: 7.6 / Method: unknown
Details: referred to 'Dijkstra, B.W.', (1978) J.Mol.Biol., 124, 53-60
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13 %protein11
2100 mMTris11
35 mM11CaCl2
4MPD120.050ml

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 9999 Å / Num. all: 7160 / Num. obs: 5435 / % possible obs: 76 % / Rmerge F obs: 0.062

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor Rwork: 0.174 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 1 86 1044
Refinement
*PLUS
Lowest resolution: 7.1 Å / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS

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