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- PDB-1o2e: Structure of the triple mutant (K53,56,120M) + Anisic acid comple... -

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Basic information

Entry
Database: PDB / ID: 1o2e
TitleStructure of the triple mutant (K53,56,120M) + Anisic acid complex of phospholipase A2
ComponentsPhospholipase A2
KeywordsHYDROLASE / Alpha Helix / Beta Sheet / Triple mutant / Anisic acid
Function / homology
Function and homology information


Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / innate immune response in mucosa / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-positive bacterium / signaling receptor binding / calcium ion binding / cell surface / extracellular space
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
4-METHOXYBENZOIC ACID / Phospholipase A2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsSekar, K. / Velmurugan, D. / Tsai, M.D.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structures of the free and anisic acid bound triple mutant of phospholipase A2.
Authors: Sekar, K. / Vaijayanthi Mala, S. / Yogavel, M. / Velmurugan, D. / Poi, M.J. / Vishwanath, B.S. / Gowda, T.V. / Jeyaprakash, A.A. / Tsai, M.D.
History
DepositionMar 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 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 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0093
Polymers13,8171
Non-polymers1922
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.61, 46.61, 102.68
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 13816.552 Da / Num. of mol.: 1 / Mutation: K53M, K56M and K120M (triple mutant)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pTO-A2MBL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P00593, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID / P-Anisic acid


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.28 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion method / pH: 7.2
Details: 50 mM Tris Buffer, MPD,70% MPD reservoir,17-20Mg/ml prot,5 mM CaCl2, 1 microlitre of anisic acid, pH 7.2, vapor diffusion method, temperature 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→19.8 Å / Num. all: 4108 / Num. obs: 3957 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.151
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.263 / Num. unique all: 392 / % possible all: 94.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
CNS1.1refinement
SCALEPACKdata scaling
RefinementResolution: 2.6→19.8 Å / σ(F): 0 / σ(I): 0 / Details: CNS 1.1
RfactorNum. reflection% reflection
Rfree0.241 240 -
Rwork0.187 --
all-4108 -
obs-3957 89 %
Refinement stepCycle: LAST / Resolution: 2.6→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 12 43 1009
Refine LS restraintsType: protein_rep.param (CNS 1.1) / Dev ideal: 0.006

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