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- PDB-2azy: Crystal Structure of Porcine Pancreatic Phospholipase A2 in Compl... -

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Basic information

Entry
Database: PDB / ID: 2azy
TitleCrystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Cholate
ComponentsPhospholipase A2, major isoenzyme
KeywordsHYDROLASE / Bile salt / cholate / CARBOXYLIC ESTER HYDROLASE / PLA2 / Pancreatic Enzyme
Function / homology
Function and homology information


regulation of D-glucose import / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / bile acid binding / phospholipase A2 / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity ...regulation of D-glucose import / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / bile acid binding / phospholipase A2 / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / lipid catabolic process / neutrophil chemotaxis / 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
CHOLIC ACID / Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPan, Y.H. / Bahnson, B.J. / Jain, M.K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural basis for bile salt inhibition of pancreatic phospholipase A2.
Authors: Pan, Y.H. / Bahnson, B.J.
History
DepositionSep 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4583
Polymers14,0101
Non-polymers4492
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Phospholipase A2, major isoenzyme
hetero molecules

A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9176
Polymers28,0192
Non-polymers8974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area3210 Å2
ΔGint-23 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.030, 70.030, 64.453
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-231-

CA

21A-246-

HOH

31A-427-

HOH

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Components

#1: Protein Phospholipase A2, major isoenzyme / Phosphatidylcholine 2-acylhydrolase / Group IB phospholipase A2


Mass: 14009.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: P00592, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: 8%PEG8K, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2004 / Details: mirrors
RadiationMonochromator: yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 14784 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.049 / Rsym value: 0.038 / Χ2: 1.5 / Net I/σ(I): 33
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 93.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 6 / Num. measured obs: 1333 / Rsym value: 0.255 / Χ2: 1.25 / % possible all: 93.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BO1

2bo1


Resolution: 1.9→35 Å / Cross valid method: THROUGHT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1421 9.6 %random
Rwork0.167 ---
all0.168 14784 --
obs0.167 13995 94.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 30 193 1193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramPROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:ion.paramION.TOP
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramWATER.TOP
X-RAY DIFFRACTION4MY_TOPPAR:cho.parCHO.TOP

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