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- PDB-1y6p: Crystal structure of disulfide engineered porcine pancratic phosp... -

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Basic information

Entry
Database: PDB / ID: 1y6p
TitleCrystal structure of disulfide engineered porcine pancratic phospholipase a2 to group-x isozyme
ComponentsPhospholipase A2, major isoenzyme
KeywordsHYDROLASE / Disulfide engineered PLA2 / Porcine pancratic isozyme
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
Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.1May 5, 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 / struct_conn ...database_2 / 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 / _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_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
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

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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)29,6167
Polymers29,4252
Non-polymers1915
Water3,891216
1
A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8284
Polymers14,7131
Non-polymers1163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7883
Polymers14,7131
Non-polymers762
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 area1730 Å2
ΔGint-60 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.988, 88.383, 38.560
Angle α, β, γ (deg.)90.00, 105.65, 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-terminal insertion KGESDKC (residues 125-131)
Source: (gene. exp.) Sus scrofa (pig) / Gene: PLA2G1B / Plasmid: PMAR25 / Production host: Escherichia coli (E. coli) / Strain (production host): PC2429 / References: UniProt: P00592, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.21 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Iso-Propanol, pH 7.5, 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: Feb 26, 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: 2.2→19.8 Å / Num. all: 11518 / Num. obs: 11340 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.09 / Net I/σ(I): 11.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1092 / Rsym value: 0.3 / % possible all: 96.8

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Processing

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

1fxf


Resolution: 2.25→19.8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 169796.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 541 5.3 %RANDOM
Rwork0.188 ---
all0.195 10747 --
obs0.192 10213 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.2004 Å2 / ksol: 0.325779 e/Å3
Displacement parametersBiso mean: 22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 5 216 2261
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.332.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 83 5.2 %
Rwork0.219 1523 -
obs--91 %
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

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