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- PDB-2aoz: Crystal structure of the myotoxin-II from Atropoides nummifer venom -

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Basic information

Entry
Database: PDB / ID: 2aoz
TitleCrystal structure of the myotoxin-II from Atropoides nummifer venom
ComponentsPhospholipase A2 homolog
KeywordsTOXIN / X-ray diffration / myotoxicity / phospholipase A2 / Atropoides nummifer
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / killing of cells of another organism / calcium ion binding / extracellular region
Similarity search - Function
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
Basic phospholipase A2 homolog
Similarity search - Component
Biological speciesAtropoides nummifer (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsMelo, C.C. / Murakami, M.T. / Angulo, Y. / Lomonte, B. / Arni, R.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of myotoxin II, a catalytically inactive Lys49 phospholipase A2 homologue from Atropoides nummifer venom.
Authors: Murakami, M.T. / Melo, C.C. / Angulo, Y. / Lomonte, B. / Arni, R.K.
History
DepositionAug 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8292
Polymers13,7331
Non-polymers961
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.939, 68.939, 64.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phospholipase A2 homolog / Myotoxin II


Mass: 13732.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: venom / Source: (natural) Atropoides nummifer (snake) / References: UniProt: P82950
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulfate, peg 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.08→30.36 Å / Num. all: 9671 / Num. obs: 9272 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1
Reflection shellResolution: 2.08→2.19 Å / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 1MC2

1mc2


Resolution: 2.08→30.36 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.342 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27502 466 4.8 %RANDOM
Rwork0.21895 ---
all0.2315 9671 --
obs0.22148 9203 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.485 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---1.02 Å20 Å2
3---2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.08→30.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 5 71 1022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021978
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9811323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.965120
X-RAY DIFFRACTIONr_chiral_restr0.0930.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02726
X-RAY DIFFRACTIONr_nbd_refined0.2280.3491
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.597
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.320.59
X-RAY DIFFRACTIONr_mcbond_it0.4981.5604
X-RAY DIFFRACTIONr_mcangle_it0.9072969
X-RAY DIFFRACTIONr_scbond_it1.653374
X-RAY DIFFRACTIONr_scangle_it2.4714.5354
LS refinement shellResolution: 2.08→2.135 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.366 35
Rwork0.292 616
Refinement TLS params.Method: refined / Origin x: 6.6742 Å / Origin y: 51.0798 Å / Origin z: 27.8042 Å
111213212223313233
T0.2533 Å2-0.0055 Å20.0362 Å2-0.1437 Å2-0.0277 Å2--0.0102 Å2
L3.6222 °22.6769 °2-0.9239 °2-12.4374 °2-3.4618 °2--2.8266 °2
S0.3192 Å °-0.3187 Å °0.424 Å °1.1556 Å °-0.1445 Å °0.4308 Å °-0.453 Å °-0.0874 Å °-0.1747 Å °

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