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- PDB-1pod: STRUCTURES OF FREE AND INHIBITED HUMAN SECRETORY PHOSPHOLIPASE A2... -

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Basic information

Entry
Database: PDB / ID: 1pod
TitleSTRUCTURES OF FREE AND INHIBITED HUMAN SECRETORY PHOSPHOLIPASE A2 FROM INFLAMMATORY EXUDATE
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE
Function / homology
Function and homology information


regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / intestinal stem cell homeostasis ...regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / intestinal stem cell homeostasis / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / phospholipase A2 / low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / calcium-dependent phospholipase A2 activity / Antimicrobial peptides / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / secretory granule / angiotensin-activated signaling pathway / phospholipid binding / positive regulation of inflammatory response / killing of cells of another organism / mitochondrial outer membrane / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / plasma membrane
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, membrane associated
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsScott, D.L. / White, S.P. / Sigler, P.B.
CitationJournal: Science / Year: 1991
Title: Structures of free and inhibited human secretory phospholipase A2 from inflammatory exudate.
Authors: Scott, D.L. / White, S.P. / Browning, J.L. / Rosa, J.J. / Gelb, M.H. / Sigler, P.B.
History
DepositionSep 7, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Jul 17, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Other / Refinement description
Category: atom_site / pdbx_database_status / software
Item: _atom_site.occupancy / _pdbx_database_status.process_site / _software.classification
Revision 2.1Aug 14, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / pdbx_validate_symm_contact / software
Item: _software.classification
Revision 2.2Oct 16, 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_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_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_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)13,9852
Polymers13,9451
Non-polymers401
Water2,756153
1
A: PHOSPHOLIPASE A2
hetero molecules

A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9704
Polymers27,8902
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+7/61
Unit cell
Length a, b, c (Å)76.300, 76.300, 90.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-289-

HOH

21A-303-

HOH

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13945.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P14555, 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


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
25 mM1dropCaCl2
30.1 MTris-HCl1drop
42.5 M1dropNaCl
50.5 mMbeta-octyl-glucopyranoside1drop
64.9 M1reservoirNaCl
70.1 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.193 / Rfactor obs: 0.193 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 1 153 1120
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.3

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