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- PDB-3fvi: Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates -

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Basic information

Entry
Database: PDB / ID: 3fvi
TitleCrystal Structure of Complex of Phospholipase A2 with Octyl Sulfates
ComponentsPhospholipase A2, major isoenzyme
KeywordsHYDROLASE / Phospholipase A2 / Pla2-1B / octyl sulfate binding / protein detergent aggregates / Lipid degradation / Lipoprotein / Metal-binding / Palmitate / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


positive regulation of podocyte apoptotic process / regulation of D-glucose import / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / calcium-dependent phospholipase A2 activity ...positive regulation of podocyte apoptotic process / regulation of D-glucose import / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / neutrophil mediated immunity / phospholipase A2 / bile acid binding / calcium-dependent 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 / positive regulation of MAP kinase activity / phospholipid binding / cellular response to insulin stimulus / fatty acid biosynthetic process / positive regulation of immune response / positive regulation of fibroblast proliferation / positive regulation of NF-kappaB transcription factor activity / 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 / 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
octyl sulfate / Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPan, Y.H.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: Structure of a premicellar complex of alkyl sulfates with the interfacial binding surfaces of four subunits of phospholipase A2.
Authors: Pan, Y.H. / Bahnson, B.J.
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

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Assembly

Deposited unit
A: Phospholipase A2, major isoenzyme
B: Phospholipase A2, major isoenzyme
C: Phospholipase A2, major isoenzyme
D: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,80423
Polymers56,0394
Non-polymers2,76619
Water1,17165
1
A: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2954
Polymers14,0101
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6785
Polymers14,0101
Non-polymers6684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8876
Polymers14,0101
Non-polymers8775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phospholipase A2, major isoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9458
Polymers14,0101
Non-polymers9367
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.988, 82.061, 123.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 14009.714 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: pancreas / Production host: Escherichia coli (E. coli) / References: UniProt: P00592, phospholipase A2

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Non-polymers , 5 types, 84 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-OSF / octyl sulfate


Mass: 209.283 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H17O4S
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, 8% w/v PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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: Jun 10, 2003 / Details: mirrors
RadiationMonochromator: Ni Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→33.54 Å / Num. all: 19134 / Num. obs: 18967 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.093 / Net I/σ(I): 15.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1823 / Rsym value: 0.415 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FXF

1fxf


Resolution: 2.7→33.54 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 178032.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 786 4.9 %RANDOM
Rwork0.206 ---
all0.209 19083 --
obs0.206 15969 83.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.4417 Å2 / ksol: 0.326809 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→33.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 163 65 4112
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it1.52
X-RAY DIFFRACTIONc_scangle_it2.282.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 89 4.4 %
Rwork0.305 1941 -
obs-1157 65.2 %
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:c8s.parMY_TOPPAR:c8s.top

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