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- PDB-1fx9: CARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + MJ33 INHIBITOR... -

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Basic information

Entry
Database: PDB / ID: 1fx9
TitleCARBOXYLIC ESTER HYDROLASE COMPLEX (DIMERIC PLA2 + MJ33 INHIBITOR + SULPHATE IONS)
ComponentsPHOSPHOLIPASE A2, MAJOR ISOENZYME
KeywordsHYDROLASE / ENZYME / CARBOXYLIC ESTER HYDROLASE / DIMER / SULPHATE BINDING / INHIBITOR BINDING
Function / homology
Function and homology information


Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Acyl chain remodelling of PI / Acyl chain remodelling of PG / Synthesis of PA / positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / phospholipid metabolic process / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / phospholipid binding / positive regulation of MAP kinase activity / cellular response to insulin stimulus / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / positive regulation of immune response / positive regulation of NF-kappaB transcription factor activity / intracellular signal transduction / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / 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, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MJI / Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPan, Y.H. / Epstein, T.M. / Jain, M.K. / Bahnson, B.J.
CitationJournal: Biochemistry / Year: 2001
Title: Five coplanar anion binding sites on one face of phospholipase A2: relationship to interface binding.
Authors: Pan, Y.H. / Epstein, T.M. / Jain, M.K. / Bahnson, B.J.
History
DepositionSep 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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, MAJOR ISOENZYME
B: PHOSPHOLIPASE A2, MAJOR ISOENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,07210
Polymers28,0192
Non-polymers1,0538
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-122 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.987, 64.987, 62.766
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein PHOSPHOLIPASE A2, MAJOR ISOENZYME / / PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE / PLA2


Mass: 14009.714 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MJI / 1-HEXADECYL-3-TRIFLUOROETHYL-SN-GLYCERO-2-PHOSPHATE METHANE / MJ33 INHIBITOR


Mass: 492.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H44F3O6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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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: 2 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.6
Details: 25% PEG3500, 0.2 M SODIUM SULPHATE, 0.1 M SODIUM ACETATE BUFFER, PH 4.6, EVAPORATION, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
23 mMMJ331drop
310 mM1dropCaCl2
425 %PEG33501drop
50.1 Msodium acetate1drop
60.2 Mammonium sulfate1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 22, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30.44 Å / Num. all: 122013 / Num. obs: 19393 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1996 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 122013 / Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4P2P

4p2p


Resolution: 2→8 Å / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: MEROHEDRAL TWINNING REFINEMENT USING SHELXL-97. XPLOR-3.1, SHELXL-97 were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 954 -RANDOM
Rwork0.171 ---
all-18138 --
obs-18138 100 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 59 185 2186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.023
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d

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