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- PDB-1y6o: Crystal structure of disulfide engineered porcine pancreatic phos... -

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Basic information

Entry
Database: PDB / ID: 1y6o
TitleCrystal structure of disulfide engineered porcine pancreatic phospholipase A2 to group-X isozyme in complex with inhibitor MJ33 and phosphate ions
ComponentsPhospholipase A2, major isoenzyme
KeywordsHYDROLASE / Hydrolase. Disulfide engineered PLA2. Porcine pancratic isozyme.
Function / homology
Function and homology information


regulation of D-glucose import across plasma membrane / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / A2-type glycerophospholipase activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / bile acid binding / phospholipase A2 / : ...regulation of D-glucose import across plasma membrane / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / A2-type glycerophospholipase activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / bile acid binding / phospholipase A2 / : / positive regulation of calcium ion transport into cytosol / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / phospholipid binding / cellular response to insulin stimulus / positive regulation of fibroblast proliferation / positive regulation of immune response / 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, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain / Phospholipase A2 ...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 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MJI / PHOSPHATE ION / Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYu, B.Z. / Pan, Y.H. / Jassen, M.J.W. / Bahnson, B.J. / Jain, M.K.
Citation
Journal: Biochemistry / Year: 2005
Title: Kinetic and structural properties of disulfide engineered phospholipase a(2): insight into the role of disulfide bonding patterns.
Authors: Yu, B.Z. / Pan, Y.H. / Janssen, M.J.W. / Bahnson, B.J. / Jain, M.K.
#1: Journal: Eur.J.Biochem. / Year: 1999
Title: Engineeering the disulphide bond patterns of secretory phospolipases A2 into porcine pancratic isozyme. The effects on folding, stability and enzymatic properties
Authors: Janssen, M.J. / Verheij, H.M. / Slotboom, A.J. / Egmond, M.R.
#2: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of human group X secreted phospholipase A2. Electrostatically neutral interfacial surface targets zwitterionic membranes
Authors: Pan, Y.H. / Yu, B.Z. / Singer, A.G. / Ghomashchi, F. / Lambeau, G. / Jain, M.K. / Bahnson, B.J.
History
DepositionDec 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE C-terminal extension (residues 125-131) KGESDKC were added to model the disulfide bonding ...SEQUENCE C-terminal extension (residues 125-131) KGESDKC were added to model the disulfide bonding pattern of the group X enzyme.

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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)31,25014
Polymers29,4252
Non-polymers1,82512
Water3,711206
1
A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7208
Polymers14,7131
Non-polymers1,0077
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5306
Polymers14,7131
Non-polymers8185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-87 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.534, 85.921, 38.554
Angle α, β, γ (deg.)90.00, 94.76, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two biological units: chain A and B.

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Components

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


Mass: 14712.515 Da / Num. of mol.: 2 / Mutation: M8L,M20L, N50C, c-terminal insertion KGESDKC
Source method: isolated from a genetically manipulated source
Details: M8L,M20L, N50C, c-termial insertion KGESDKC (residues 125 to 131)
Source: (gene. exp.) Sus scrofa (pig) / Gene: PLA2G1B / Plasmid: pMAR25 / Production host: Escherichia coli (E. coli) / Strain (production host): PC2429
Keywords: M8L,M20L, N50C, c-termial insertion KGESDKC (residues 125 to 131)
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MJI / 1-HEXADECYL-3-TRIFLUOROETHYL-SN-GLYCERO-2-PHOSPHATE METHANE / MJ33 INHIBITOR


Mass: 492.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H44F3O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.45 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Potassium phosphate, PEG 8000, , pH 6.5, VAPOR DIFFUSION, HANGING DROP, 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: Oct 22, 2001 / Details: Mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→28.6 Å / Num. all: 16950 / Num. obs: 14222 / % possible obs: 83.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.045 / Net I/σ(I): 17
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1398 / Rsym value: 0.293 / % possible all: 83.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FXF

1fxf


Resolution: 2→28.64 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 427212.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Atoms C2-C16 in residue 217 and atoms C4-C16 in residue 218 were deleted from the model due to disorder.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 717 5 %RANDOM
Rwork0.196 ---
obs0.196 14222 83.8 %-
all-16950 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2197 Å2 / ksol: 0.383718 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0.27 Å2
2---0.19 Å20 Å2
3----0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 78 206 2324
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.592
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.472.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 98 4.5 %
Rwork0.248 2057 -
obs--76.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MY_TOPPAR:MJ33_13.PARMY_TOPPAR:MJ33_C13.TOP
X-RAY DIFFRACTION5MY_TOPPAR:MJ33_C11.PARMY_TOPPAR:MJ33_C11.TOP

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