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- PDB-3iq3: Crystal Structure of Bothropstoxin-I complexed with polietilene g... -

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Basic information

Entry
Database: PDB / ID: 3iq3
TitleCrystal Structure of Bothropstoxin-I complexed with polietilene glicol 4000 - 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 / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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: 1.55 Å
AuthorsSalvador, G.H.M. / Marchi-Salvador, D.P. / Silva, M.C.O. / Soares, A.M. / Fontes, M.R.M.
Citation
Journal: 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.
#1: Journal: To be Published
Title: Structure of Bothropstoxin-I Chemically Modified by p-Bromophenacyl Bromide Reveals Importante Structural Changes Associated With the Inhibition of Myotoxic Activity
Authors: Salvador, G.H.M. / Marchi-Salvador, D.P. / Silva, M.C.O. / Soares, A.M. / Fontes, M.R.M.
History
DepositionAug 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2 homolog bothropstoxin-1
B: Phospholipase A2 homolog bothropstoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7607
Polymers27,5042
Non-polymers1,2555
Water4,342241
1


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


Theoretical massNumber of molelcules
Total (without water)14,2994
Polymers13,7521
Non-polymers5473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Phospholipase A2 homolog bothropstoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4613
Polymers13,7521
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.500, 70.800, 43.800
Angle α, β, γ (deg.)90.00, 102.20, 90.00
Int Tables number4
Space group name H-MP1211

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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: 13752.150 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Venom Glands / Source: (natural) Bothrops jararacussu (jararacussu) / References: UniProt: Q90249
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsD TO N CONFLICT IN UNP ENTRY Q90249

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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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 29% PEG 4000, 0.1M Tris HCl, 0.2M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.425 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL - Si curved crystal asymmetrically-cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 32689 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 12.73
Reflection shellResolution: 1.55→1.62 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.82 / Rsym value: 0.439 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry (3HZD)

3hzd


Resolution: 1.55→18.32 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.573 / SU ML: 0.074 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24647 1652 5.1 %RANDOM
Rwork0.20049 ---
obs0.20291 30990 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.019 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.107 Å0.146 Å
Luzzati d res low-4.621 Å
Refinement stepCycle: LAST / Resolution: 1.55→18.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 82 241 2229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222037
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6322.0172712
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86523.84678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60215376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7521510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021442
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2490.21412
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.21434
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2304
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1951.51219
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77821922
X-RAY DIFFRACTIONr_scbond_it3.8643912
X-RAY DIFFRACTIONr_scangle_it44.5790
X-RAY DIFFRACTIONr_rigid_bond_restr3.80532131
X-RAY DIFFRACTIONr_sphericity_free5.263241
X-RAY DIFFRACTIONr_sphericity_bonded2.98731988
LS refinement shellResolution: 1.55→1.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 124 -
Rwork0.258 2299 -
obs--99.43 %

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