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- PDB-1pa0: CRYSTAL STRUCTURE OF BNSP-7, A LYS49-PHOSPHOLIPASE A2 -

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Basic information

Entry
Database: PDB / ID: 1pa0
TitleCRYSTAL STRUCTURE OF BNSP-7, A LYS49-PHOSPHOLIPASE A2
ComponentsMyotoxic phospholipase A2-like
KeywordsHYDROLASE / Lys49-phospholipase A2 / myotoxin / bothropic venom
Function / homology
Function and homology information


phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / 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
Basic phospholipase A2 homolog BnSP-7
Similarity search - Component
Biological speciesBothrops neuwiedi pauloensis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMagro, A.J. / Soares, A.M. / Giglio, J.R. / Fontes, M.R.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Crystal structures of BnSP-7 and BnSP-6, two Lys49-phospholipases A(2): quaternary structure and inhibition mechanism insights.
Authors: Magro, A.J. / Soares, A.M. / Giglio, J.R. / Fontes, M.R.
#1: Journal: Biochim.Biophys.Acta / Year: 1999
Title: Crystallization and preliminary X-ray diffraction analysis of a myotoxic phospholipase A2 homologue from Bothrops neuwiedi pauloensis venom
Authors: Fontes, M.R. / Soares, A.M. / Rodrigues, V.M. / Fernandes, A.C. / Da Silva, R.J. / Giglio, J.R.
#2: Journal: Arch.Biochem.Biophys. / Year: 2000
Title: Structural and Function Characterization of BnSP-7, a Lys49 Myotoxic Phospholipase A2 Homologue from Bothrops neuwiedi Venom
Authors: Soares, A.M. / Guerra-Sa, R. / Borja-Oliveira, C.R. / Rodrigues, V.M. / Rodrigues-Simioni, L. / Rodrigues, V. / Fontes, M.R. / Lomonte, B. / Gutirrez, J.M. / Giglio, J.R.
History
DepositionMay 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQRES Author states there are a few natural mutations in the sequence found in the GenBank ...SEQRES Author states there are a few natural mutations in the sequence found in the GenBank database. This sequence was obtained by cDNA sequence and the natural mutations are due to protein isoforms found in the B. neuwiedi pauloensis venom.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myotoxic phospholipase A2-like
B: Myotoxic phospholipase A2-like


Theoretical massNumber of molelcules
Total (without water)27,5042
Polymers27,5042
Non-polymers00
Water7,152397
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.330, 57.330, 130.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe monomer B is related to monomer A by two fold axis: -x,-y,z

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Components

#1: Protein Myotoxic phospholipase A2-like


Mass: 13752.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Venom glands / Source: (natural) Bothrops neuwiedi pauloensis (snake) / Species: Bothrops neuwiedi / Strain: pauloensis / References: UniProt: Q9IAT9, phospholipase A2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 6000, ammonium sulphate, sodium cacodilate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 2002 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 13254 / Num. obs: 13254 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1525 / % possible all: 95.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BthTX-I (closed form)

Resolution: 2.2→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 641 -RANDOM
Rwork0.208 ---
obs-12489 94.5 %-
Displacement parametersBiso mean: 38.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 0 397 2261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.66
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.031
RfactorNum. reflection% reflection
Rfree0.311 98 -
Rwork0.254 --
obs-1931 95.8 %

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