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- PDB-3i3i: Crystal Structure of Bothropstoxin-I crystallized at 283 K -

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Basic information

Entry
Database: PDB / ID: 3i3i
TitleCrystal Structure of Bothropstoxin-I crystallized at 283 K
ComponentsPhospholipase A2 homolog bothropstoxin-1
KeywordsTOXIN / Homologue Phospholipase A2 / Bothropstoxin-I / BthTX-I_10C / Lys49-PLA2 from Bothrops jararacussu / Snake venom / Antibiotic / Antimicrobial / Disulfide bond / Myotoxin / Secreted
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / heparin binding / 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 bothropstoxin-I
Similarity search - Component
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsSalvador, G.H.M. / Marchi-Salvador, D.P. / Soares, A.M. / Fontes, M.R.M.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Comparison between apo and complexed structures of bothropstoxin-I reveals the role of Lys122 and Ca(2+)-binding loop region for the catalytically inactive Lys49-PLA(2)s.
Authors: Fernandes, C.A. / Marchi-Salvador, D.P. / Salvador, G.M. / Silva, M.C. / Costa, T.R. / Soares, A.M. / Fontes, M.R.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Nov 30, 2011Group: Database references
Revision 1.4Apr 4, 2012Group: Database references
Revision 1.5Sep 6, 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

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Assembly

Deposited unit
A: Phospholipase A2 homolog bothropstoxin-1


Theoretical massNumber of molelcules
Total (without water)13,7531
Polymers13,7531
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phospholipase A2 homolog bothropstoxin-1

A: Phospholipase A2 homolog bothropstoxin-1


Theoretical massNumber of molelcules
Total (without water)27,5062
Polymers27,5062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1050 Å2
ΔGint-13 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.755, 80.044, 67.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Phospholipase A2 homolog bothropstoxin-1 / Phospholipase A2 homolog 1 / Bothropstoxin I / BthTX-I / BtxtxI / BOJU-I / Myotoxic phospholipase A2-like


Mass: 13753.136 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: venom glands / Source: (natural) Bothrops jararacussu (jararacussu) / References: UniProt: Q90249
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% Isopropanol, 18% PEG 4000, 0.1M Na Citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 3, 2007 / Details: mirrors
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 14091 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 15.77
Reflection shellResolution: 1.82→1.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.309 / % possible all: 92.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HZD

3hzd


Resolution: 1.82→25.83 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1406374.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 705 5 %RANDOM
Rwork0.158 ---
obs0.158 14022 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.6042 Å2 / ksol: 0.365754 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2---0.46 Å20 Å2
3---2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.82→25.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 0 260 1213
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.032
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_deg2.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.641.5
X-RAY DIFFRACTIONc_mcangle_it6.532
X-RAY DIFFRACTIONc_scbond_it7.822
X-RAY DIFFRACTIONc_scangle_it9.62.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.82→1.93 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 103 4.7 %
Rwork0.257 2101 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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