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- PDB-4dbk: Crystal structure of porcine pancreatic phospholipase A2 complexe... -

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Basic information

Entry
Database: PDB / ID: 4dbk
TitleCrystal structure of porcine pancreatic phospholipase A2 complexed with berberine
ComponentsPhospholipase A2, major isoenzyme
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Monomeric protein / berberine / HYDROLASE-HYDROLASE INHIBITOR complex
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 / phosphatidylcholine metabolic process ...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 / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / calcium-dependent phospholipase A2 activity / neutrophil mediated immunity / phospholipase A2 / bile acid binding / positive regulation of calcium ion transport into cytosol / phospholipid metabolic process / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / positive regulation of MAP kinase activity / phospholipid binding / fatty acid biosynthetic process / cellular response to insulin stimulus / positive regulation of immune response / positive regulation of fibroblast proliferation / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / 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, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BERBERINE / Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNaveen, C.D. / Abhilash, J. / Prasanth, G.K. / Sadasivan, C. / Haridas, M.
CitationJournal: To be Published
Title: Crystal structure of porcine pancreatic phospholipase A2 complexed with berberine
Authors: Naveen, C.D. / Abhilash, J. / Prasanth, G.K. / Sadasivan, C. / Haridas, M.
History
DepositionJan 16, 2012Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 25, 2012ID: 3L69, 3TT5
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4264
Polymers14,0101
Non-polymers4173
Water1,910106
1


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

A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8528
Polymers28,0192
Non-polymers8336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2140 Å2
ΔGint-77 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.600, 68.600, 70.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 14009.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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: Chemical ChemComp-BER / BERBERINE / Berberine


Mass: 336.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18NO4 / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.05M Tris maleate buffer, 5mM CaCl2, 16% MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 26, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→49 Å / Num. obs: 7686 / % possible obs: 98.1 %

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4P2P

4p2p


Resolution: 2.3→9.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.172 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25313 391 4.8 %RANDOM
Rwork0.18455 ---
obs0.18767 7686 93.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.444 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→9.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 27 106 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221029
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9731399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7415123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.3982550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.24115163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.948154
X-RAY DIFFRACTIONr_chiral_restr0.1140.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021803
X-RAY DIFFRACTIONr_mcbond_it0.9071.5619
X-RAY DIFFRACTIONr_mcangle_it1.6982993
X-RAY DIFFRACTIONr_scbond_it2.5583410
X-RAY DIFFRACTIONr_scangle_it4.0564.5406
LS refinement shellResolution: 2.301→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 42 -
Rwork0.221 566 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: 35.3129 Å / Origin y: -14.1543 Å / Origin z: -2.5174 Å
111213212223313233
T0.1205 Å2-0.0883 Å20.0348 Å2-0.1195 Å20.0159 Å2--0.1024 Å2
L0.4057 °20.2442 °2-0.5143 °2-5.8058 °2-1.6707 °2--1.5185 °2
S0.1042 Å °-0.1117 Å °-0.0782 Å °0.2499 Å °-0.4357 Å °-0.1864 Å °0.0245 Å °0.1444 Å °0.3315 Å °

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