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- PDB-1pc9: Crystal Structure of BnSP-6, a Lys49-Phospholipase A2 -

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Basic information

Entry
Database: PDB / ID: 1pc9
TitleCrystal Structure of BnSP-6, a Lys49-Phospholipase A2
ComponentsBnSP-6
KeywordsHYDROLASE / Lys49-phospholipase A2 / myotoxin / Bothrops / 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: 2.5 Å
AuthorsMagro, A.J. / Soares, A.M. / Giglio, J.R. / Fontes, M.R.M.
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.M.
#1: Journal: Protein Pept.Lett. / Year: 2000
Title: Crystallization and Preliminary X-Ray Diffraction Studies of BnSP-6, a Myotoxic Phospholipase A2 from Bothrops neuwiedi Venom
Authors: Fontes, M.R.M. / Monteiro, L.E. / Soares, A.M. / Rodrigues, V.M. / da Silva, R.J. / Giglio, J.R.
History
DepositionMay 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 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 999sequence An appropriate sequence database reference was not available at the time of processing this structure

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BnSP-6
B: BnSP-6


Theoretical massNumber of molelcules
Total (without water)27,3622
Polymers27,3622
Non-polymers00
Water4,107228
1
A: BnSP-6


Theoretical massNumber of molelcules
Total (without water)13,6811
Polymers13,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BnSP-6


Theoretical massNumber of molelcules
Total (without water)13,6811
Polymers13,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.670, 57.670, 130.130
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 BnSP-6


Mass: 13681.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops neuwiedi pauloensis (snake) / Organ: Venom glands / Species: Bothrops neuwiedi / Strain: pauloensis / References: UniProt: Q9IAT9, phospholipase A2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 46.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, ammonium sulphate, sodium cacodilate., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 4, 1999
RadiationMonochromator: Mirrors. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 9269 / Num. obs: 8429 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 8.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 1.6 / Num. unique all: 885 / % possible all: 90.2

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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: 2.5→26.4 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 430 -random
Rwork0.186 ---
obs-8389 91.6 %-
Displacement parametersBiso mean: 40.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 0 228 2092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.043
RfactorNum. reflection% reflection
Rfree0.338 62 -
Rwork0.246 --
obs-1258 90.5 %

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