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- PDB-1xxs: Structural insights for fatty acid binding in a Lys49 phospholipa... -

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Entry
Database: PDB / ID: 1xxs
TitleStructural insights for fatty acid binding in a Lys49 phospholipase A2: crystal structure of myotoxin II from Bothrops moojeni complexed with stearic acid
ComponentsPhospholipase A2 homolog 2
KeywordsHYDROLASE / phospholipase A2 / stearic acid / dimer interface / fatty acid binding
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonic acid secretion / defense response to fungus / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / killing of cells of another organism / defense response to bacterium ...calcium-dependent phospholipase A2 activity / arachidonic acid secretion / defense response to fungus / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / killing of cells of another organism / defense response to bacterium / calcium ion binding / 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
STEARIC ACID / Basic phospholipase A2 homolog myotoxin II
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWatanabe, L. / Soares, A.M. / Ward, R.J. / Fontes, M.R. / Arni, R.K.
Citation
Journal: Biochimie / Year: 2005
Title: Structural insights for fatty acid binding in a Lys49-phospholipase A(2): crystal structure of myotoxin II from Bothrops moojeni complexed with stearic acid
Authors: Watanabe, L. / Soares, A.M. / Ward, R.J. / Fontes, M.R. / Arni, R.K.
#1: Journal: PROTEIN PEPT.LETT. / Year: 2003
Title: Initiating structural studies of Lys49-PLA2 homologues complexed with an anionic detergent, a fatty acid and a natural lipid
Authors: Watanabe, L. / Fontes, M.R. / Soares, A.M. / Giglio, J.R. / Arni, R.K.
#2: Journal: Arch.Biochem.Biophys. / Year: 2000
Title: Structural and functional characterization of myotoxin I, a Lys49 phospholipase A(2) homologue from Bothrops moojeni (Caissaca) snake venom
Authors: Soares, A.M. / Andriao-Escarso, S.H. / Angulo, Y. / Lomonte, B. / Gutierrez, J.M. / Marangoni, S. / Toyama, M.H. / Arni, R.K. / Giglio, J.R.
#3: Journal: Toxicon / Year: 1998
Title: A rapid procedure for the isolation of the Lys-49 myotoxin II from Bothrops moojeni (caissaca) venom: biochemical characterization, crystallization, myotoxic and edematogenic activity
Authors: Soares, A.M. / Rodrigues, V.M. / Homsi-Brandeburgo, M.I. / Toyama, M.H. / Lombardi, F.R. / Arni, R.K. / Giglio, J.R.
#4: Journal: PROTEIN PEPT.LETT. / Year: 1997
Title: Crystal Structure of miotoxin-II: a myotoxic phospholipase A2 homologue from Bothrops moojeni venom
Authors: de Azevedo Jr., W.F. / Ward, R.J. / Lombardi, F.R. / Giglio, J.R. / Soares, A.M. / Fontes, M.R.M. / Arni, R.K.
History
DepositionNov 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN STE 205 AND STE 206 ARE BOUND AT THE DIMER INTERFACE OF THE PROTEIN. THEY ARE RELATED BY ...HETEROGEN STE 205 AND STE 206 ARE BOUND AT THE DIMER INTERFACE OF THE PROTEIN. THEY ARE RELATED BY TWO-FOLD SYMMETRY AND SHARE THE SAME SITE. THESE MOLECULES WERE REFINED WITH PARTIAL OCCUPANCIES (0.5).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 homolog 2
B: Phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,85913
Polymers27,6722
Non-polymers2,18711
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.180, 88.710, 51.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phospholipase A2 homolog 2 / Myotoxin II / MjTX-II / M-VI


Mass: 13836.114 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: venom glands / Source: (natural) Bothrops moojeni (Brazilian lancehead) / References: UniProt: Q9I834, phospholipase A2
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-STE / STEARIC ACID / Stearic acid


Mass: 284.477 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H36O2

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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: 2.58 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.6-0.8 M sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1999
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.8→15.4 Å / Num. all: 21341 / Num. obs: 21341 / % possible obs: 80.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 0.221 / Num. unique all: 2787 / % possible all: 66.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MjTX-II native

Resolution: 1.8→15.4 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1047 -RANDOM
Rwork0.166 ---
all0.17 21341 --
obs0.17 21341 80.7 %-
Displacement parametersBiso mean: 35.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.8→15.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 133 0 2049
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_mcbond_it0.006
X-RAY DIFFRACTIONx_mcangle_it1.2
X-RAY DIFFRACTIONx_dihedral_angle_d21.3
X-RAY DIFFRACTIONx_improper_angle_d0.68

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