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- PDB-2phi: A LARGE CONFORMATIONAL CHANGE IS FOUND IN THE CRYSTAL STRUCTURE O... -

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Basic information

Entry
Database: PDB / ID: 2phi
TitleA LARGE CONFORMATIONAL CHANGE IS FOUND IN THE CRYSTAL STRUCTURE OF THE PORCINE PANCREATIC PHOSPHOLIPASE A2 POINT MUTANT F63V
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE (CARBOXYLIC ESTER)
Function / homology
Function and homology information


positive regulation of podocyte apoptotic process / regulation of D-glucose import / phospholipase A2 activity / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / calcium-dependent phospholipase A2 activity ...positive regulation of podocyte apoptotic process / regulation of D-glucose import / phospholipase A2 activity / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / calcium-dependent phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / lipid catabolic process / neutrophil chemotaxis / positive regulation of MAP kinase activity / 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: 2.2 Å
AuthorsDijkstra, B.W. / Thunnissen, M.M.G.M. / Kalk, K.H. / Drenth, J.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structure of a porcine pancreatic phospholipase A2 mutant. A large conformational change caused by the F63V point mutation.
Authors: Thunnissen, M.M. / Franken, P.A. / de Haas, G.H. / Drenth, J. / Kalk, K.H. / Verheij, H.M. / Dijkstra, B.W.
#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: FEBS Lett. / Year: 1983
Title: Polypeptide Chains with Similar Amino Acid Sequences But a Distinctly Different Conformation. Bovine and Porcine Phospholipase A2
Authors: Dijkstra, B.W. / Weijer, W.J. / Wierenga, R.K.
#3: 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.
History
DepositionApr 8, 1993Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 25, 2012Group: Database references
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
B: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0445
Polymers27,9232
Non-polymers1203
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-39 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.880, 65.230, 52.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CALCIUM 1 LIES ON A NONCRYSTALLOGRAPHIC LOCAL TWO-FOLD AXIS.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998134, 0.005944, -0.060766), (0.006402, 0.999953, -0.007342), (0.06072, -0.007717, -0.998125)
Vector: 121.967, -0.422, 74.087)
DetailsTHE ENZYME CRYSTALLIZES AS A DIMER IN THE ASYMMETRIC UNIT. THE TRANSFORMATION GIVEN ON *MTRIX* RECORDS BELOW YIELDS OPTIMAL CARBON-ALPHA COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE RMS DIFFERENCE FOR ALL 124 CARBON-ALPHA PAIRS IS 0.526 ANGSTROMS, 0.153 FOR THE 93 CARBON-ALPHA PAIRS WHEN THE MOST DEVIATING PAIRS ARE REMOVED.

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13961.671 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00592, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.87 %

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.176 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 3 195 2132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg

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