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- PDB-2oqd: Crystal Structure of BthTX-II -

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Basic information

Entry
Database: PDB / ID: 2oqd
TitleCrystal Structure of BthTX-II
ComponentsPhospholipase A2
KeywordsHYDROLASE / Asp49-Phospholipase A2 / BthTX-II / Bothropstoxin II / Bothrops jararacussu
Function / homology
Function and homology information


phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / 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 bothropstoxin-II
Similarity search - Component
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsCorrea, L.C. / Marchi-Salvador, D.P. / Cintra, A.C.O. / Soares, A.M. / Fontes, M.R.M.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Crystal structure of a myotoxic Asp49-phospholipase A(2) with low catalytic activity: Insights into Ca(2+)-independent catalytic mechanism.
Authors: Correa, L.C. / Marchi-Salvador, D.P. / Cintra, A.C. / Sampaio, S.V. / Soares, A.M. / Fontes, M.R.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2
B: Phospholipase A2


Theoretical massNumber of molelcules
Total (without water)28,0302
Polymers28,0302
Non-polymers00
Water4,161231
1
A: Phospholipase A2

A: Phospholipase A2


Theoretical massNumber of molelcules
Total (without water)28,0302
Polymers28,0302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1260 Å2
MethodPISA
2
B: Phospholipase A2

B: Phospholipase A2


Theoretical massNumber of molelcules
Total (without water)28,0302
Polymers28,0302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.912, 98.458, 46.720
Angle α, β, γ (deg.)90.00, 125.89, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer generated from the dimer in the asymmetric unit.

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Components

#1: Protein Phospholipase A2 / Phosphatidylcholine 2- acylhydrolase / BJUPLA2


Mass: 14015.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Gland venom / Source: (natural) Bothrops jararacussu (jararacussu) / References: UniProt: P45881, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 1.96 Å3/Da / Density % sol: 37.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% 2-propanol, 13% PEG 4000, 0.1M 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: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 10, 2006 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.19→40 Å / Num. all: 10657 / Num. obs: 10657 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.109 / Net I/σ(I): 11.3
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.05 / Rsym value: 0.492 / % possible all: 92.9

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Processing

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

1gmz


Resolution: 2.19→30.01 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1526649 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 555 5.2 %RANDOM
Rwork0.207 ---
obs0.207 10657 95.9 %-
all-10657 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.4515 Å2 / ksol: 0.310762 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å20 Å210.61 Å2
2---13.32 Å20 Å2
3---9.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.19→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 0 231 2122
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.19→2.33 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 98 5.7 %
Rwork0.359 1619 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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