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- PDB-4p2p: AN INDEPENDENT CRYSTALLOGRAPHIC REFINEMENT OF PORCINE PHOSPHOLIPA... -

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Basic information

Entry
Database: PDB / ID: 4p2p
TitleAN INDEPENDENT CRYSTALLOGRAPHIC REFINEMENT OF PORCINE PHOSPHOLIPASE A2 AT 2.4 ANGSTROMS RESOLUTION
ComponentsPHOSPHOLIPASE A2
KeywordsCARBOXYLIC ESTER HYDROLASE
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: 2.4 Å
AuthorsFinzel, B.C. / Ohlendorf, D.H. / Weber, P.C. / Salemme, F.R.
CitationJournal: Acta Crystallogr.,Sect.B / Year: 1991
Title: An independent crystallographic refinement of porcine phospholipase A2 at 2.4 A resolution
Authors: Finzel, B.C. / Ohlendorf, D.H. / Weber, P.C. / Salemme, F.R.
History
DepositionOct 22, 1991Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 6, 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_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
Water1448
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 operation6_765-x+2,-x+y+1,-z+1/31
Buried area1510 Å2
ΔGint-50 kcal/mol
Surface area13500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.400, 69.400, 70.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: LIMITED ELECTRON DENSITY WAS FOUND FOR RESIDUES HIS 17, PRO 18, LEU 19, MET 20, ASP 21, GLU 81 AND LYS 113.
2: CALCIUM ION 202 LIES ON THE CRYSTALLOGRAPHIC TWO-FOLD AXIS AND HAS AN OCCUPANCY OF 0.5.
Components on special symmetry positions
IDModelComponents
11A-202-

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.: 8 / 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: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal grow
*PLUS
Method: unknown / pH: 7.2 / Details: Drenth, J., (1976) Nature(London), 264, 373.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1enzyme11
20.05 MTris maleate11
35 mM11CaCl2
4methanol11can be replaced with MPD

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Num. all: 8020 / Num. obs: 8006 / Observed criterion σ(I): 0.97 / Num. measured all: 42862

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→5 Å
Details: LIMITED ELECTRON DENSITY WAS FOUND FOR RESIDUES HIS 17, PRO 18, LEU 19, MET 20, ASP 21, GLU 81 AND LYS 113.
RfactorNum. reflection
obs0.21 6382
Refinement stepCycle: LAST / Resolution: 2.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 2 8 981
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.03
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8411
X-RAY DIFFRACTIONp_mcangle_it1.5382
X-RAY DIFFRACTIONp_scbond_it1.3731.5
X-RAY DIFFRACTIONp_scangle_it2.3653
X-RAY DIFFRACTIONp_plane_restr0.0130.03
X-RAY DIFFRACTIONp_chiral_restr0.2490.3
X-RAY DIFFRACTIONp_singtor_nbd0.1990.5
X-RAY DIFFRACTIONp_multtor_nbd0.2290.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1710.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(I): 0.1 / Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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