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- PDB-4kf3: Crystal Structure of Myotoxin II (MjTX-II), a myotoxic Lys49-phos... -

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Basic information

Entry
Database: PDB / ID: 4kf3
TitleCrystal Structure of Myotoxin II (MjTX-II), a myotoxic Lys49-phospholipase A2 from Bothrops moojeni.
ComponentsBasic phospholipase A2 homolog 2
KeywordsTOXIN / Phospholipase A2-like myotoxin / Venom glands
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
ISOPROPYL ALCOHOL / Basic phospholipase A2 homolog myotoxin II
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSalvador, G.H.M. / dos Santos, J.I. / Fontes, M.R.M.
CitationJournal: Toxicon / Year: 2013
Title: Structural and functional studies with mytoxin II from Bothrops moojeni reveal remarkable similarities and differences compared to other catalytically inactive phospholipases A2-like.
Authors: Salvador, G.H. / Cavalcante, W.L. / Dos Santos, J.I. / Gallacci, M. / Soares, A.M. / Fontes, M.R.
History
DepositionApr 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
B: Basic phospholipase A2 homolog 2
A: Basic phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,60312
Polymers27,8242
Non-polymers1,77810
Water3,333185
1
B: Basic phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1567
Polymers13,9121
Non-polymers1,2446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Basic phospholipase A2 homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4475
Polymers13,9121
Non-polymers5354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.999, 62.169, 86.007
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 Basic phospholipase A2 homolog 2 / svPLA2 homolog / M-VI / MjTX-II / Myotoxin II


Mass: 13912.211 Da / Num. of mol.: 2 / Fragment: Phospholipase A2-Like myotoxin / Source method: isolated from a natural source / Source: (natural) Bothrops moojeni (Brazilian lancehead) / References: UniProt: Q9I834
#2: Chemical
ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% (v/v) 2-propanol, 20% (w/v) polyethylene Glycol 4000 and 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.42 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 22, 2012 / Details: mirrors
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 19571 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 10.37
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.01 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XXS

1xxs


Resolution: 1.92→38.96 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 945 -Random
Rwork0.227 ---
all0.227 19491 --
obs0.227 19491 92.4 %-
Displacement parametersBiso mean: 56.13 Å2
Baniso -1Baniso -2Baniso -3
1--4.9 Å20 Å2-0 Å2
2---5.45 Å2-0 Å2
3---10.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.92→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 120 185 2178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.03
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.76

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