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- PDB-4g5i: Crystal Structure of Porcine pancreatic PlA2 in complex with DBP -

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Basic information

Entry
Database: PDB / ID: 4g5i
TitleCrystal Structure of Porcine pancreatic PlA2 in complex with DBP
ComponentsPhospholipase A2, major isoenzyme
KeywordsHYDROLASE / PHOSPHOLIPASE A2 / DISULFIDE BOND / 2 LIPID DEGRADATION / LIPOPROTEIN / METAL-BINDING / PALMITATE
Function / homology
Function and homology information


positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding ...positive regulation of podocyte apoptotic process / regulation of glucose import / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / phospholipase A2 activity / leukotriene biosynthetic process / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / 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
dibutyl benzene-1,2-dicarboxylate / Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPrasanth, G.K. / Naveen, C.D. / Mandal, P.K. / Karthe, P. / Haridas, M. / Sadasivan, C.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Porcine pancreatic PlA2 in complex with DBP
Authors: Prasanth, G.K. / Naveen, C.D. / Mandal, P.K. / Karthe, P. / Haridas, M. / Sadasivan, C.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release

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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)14,4446
Polymers14,0101
Non-polymers4345
Water1,49583
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)28,88712
Polymers28,0192
Non-polymers86810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2350 Å2
ΔGint-125 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.860, 68.860, 70.180
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.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DB7 / dibutyl benzene-1,2-dicarboxylate / Dibutyl phthalate


Mass: 278.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.05M Tris maleate buffer, 5mM Calcium chloride, 16% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 290K , pH 7.2, temperature 298.15K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 25, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→29.82 Å / Num. obs: 6808 / % possible obs: 92.49 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.038
Reflection shellResolution: 2.4→2.46 Å / % possible all: 92.49

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→9.94 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.701 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24293 326 4.6 %RANDOM
Rwork0.18241 ---
obs0.18511 6808 92.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.539 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→9.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 24 83 1078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221020
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.9611380
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0935123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.9612550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2615163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.902154
X-RAY DIFFRACTIONr_chiral_restr0.1240.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021795
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1361.5619
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1772993
X-RAY DIFFRACTIONr_scbond_it3.2033401
X-RAY DIFFRACTIONr_scangle_it5.2594.5387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 21 -
Rwork0.222 520 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 33.3384 Å / Origin y: -14.3396 Å / Origin z: 14.1777 Å
111213212223313233
T0.0602 Å20.0586 Å20.018 Å2-0.1356 Å20.0148 Å2--0.0667 Å2
L0.7757 °2-1.3383 °2-0.7365 °2-9.2526 °22.9899 °2--3.0232 °2
S0.0196 Å °0.0416 Å °-0.2095 Å °-0.0736 Å °-0.2957 Å °0.3233 Å °0.1818 Å °-0.1488 Å °0.2761 Å °

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