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- PDB-1u73: Crystal structure of a Dimeric Acidic Platelet Aggregation Inhibi... -

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Basic information

Entry
Database: PDB / ID: 1u73
TitleCrystal structure of a Dimeric Acidic Platelet Aggregation Inhibitor and Hypotensive Phospholipase A2 from Bothrops jararacussu
Componentshypotensive phospholipase A2
KeywordsHYDROLASE / acidic phospholipase A2 / Bothrops jararacussu venom / platelet aggregation and hypotensive effects / oligomeric state / dimeric
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / regulation of blood pressure / 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
Acidic phospholipase A2 BthA-1
Similarity search - Component
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMagro, A.J. / Murakami, M.T. / Soares, A.M. / Arni, R.K. / Fontes, M.R.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Crystal structure of an acidic platelet aggregation inhibitor and hypotensive phospholipase A(2) in the monomeric and dimeric states: insights into its oligomeric state
Authors: Magro, A.J. / Murakami, M.T. / Marcussi, S. / Soares, A.M. / Arni, R.K. / Fontes, M.R.
#1: Journal: Biochem.Pharm. / Year: 2002
Title: Structural and Functional Characterization of an Acidic Platelet Aggregation Inhibitor and Hypotensive Phospholipase A2 from Bothrops jararacussu Venom
Authors: Andriao-Escarso, S.H. / Soares, A.M. / Fontes, M.R. / Fuly, A.L. / Correa, F.M. / Rosa, J.C. / Greene, L.J. / Giglio, J.R.
History
DepositionAug 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: 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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypotensive phospholipase A2
B: hypotensive phospholipase A2


Theoretical massNumber of molelcules
Total (without water)27,4012
Polymers27,4012
Non-polymers00
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.193, 63.136, 47.407
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypotensive phospholipase A2


Mass: 13700.451 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Venom glands / Source: (natural) Bothrops jararacussu (jararacussu) / References: UniProt: Q8AXY1, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 1.733 Å3/Da / Density % sol: 29.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: ammonium sulfate, PEG 6000, pH 3.5, 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 15, 2002 / Details: Mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.9→29.7 Å / Num. all: 15160 / Num. obs: 14151 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 5 / Num. unique all: 2084 / % possible all: 87.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BthA-I (monomeric form)

Resolution: 1.9→29.7 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 712 -Random
Rwork0.19 ---
all-15160 --
obs-14151 93.3 %-
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å2-4.4 Å2
2---3.11 Å20 Å2
3---4.29 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 0 381 2281
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.75

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