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- PDB-3i03: Crystal structure of bothropstoxin-I chemically modified by p-bro... -

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Basic information

Entry
Database: PDB / ID: 3i03
TitleCrystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) - monomeric form at a high resolution
ComponentsPhospholipase A2 homolog bothropstoxin-1
KeywordsTOXIN / Lys49-PLA2s / Phospholipase homologue / bothropstoxin-I / p-bromophenacyl bromide / myotoxicity / Antibiotic / Antimicrobial / Disulfide bond / Myotoxin / Secreted
Function / homology
Function and homology information


phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / 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
ISOPROPYL ALCOHOL / p-Bromophenacyl bromide / Basic phospholipase A2 homolog bothropstoxin-I
Similarity search - Component
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsMarchi-Salvador, D.P. / Fernandes, C.A.H. / 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 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Feb 22, 2012Group: Database references
Revision 2.0Nov 27, 2019Group: Advisory / Derived calculations ...Advisory / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0913
Polymers13,7531
Non-polymers3382
Water6,323351
1
A: Phospholipase A2 homolog bothropstoxin-1
hetero molecules

A: Phospholipase A2 homolog bothropstoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1826
Polymers27,5062
Non-polymers6764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1410 Å2
ΔGint-15.7 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.846, 78.294, 66.615
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: The bothropstoxin-I was isolated from Bothrops jararacussu venom.
Source: (natural) Bothrops jararacussu (jararacussu) / Tissue: venom / References: UniProt: Q90249
#2: Chemical ChemComp-PBP / p-Bromophenacyl bromide


Mass: 277.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6Br2O
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 20% w/v PEG 4000, 20% v/v Isopropanol, 0.1 M Sodium citrate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.425 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2007
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 22361 / Num. obs: 22198 / % possible obs: 99.27 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 24.8 Å2
Reflection shellResolution: 1.48→1.53 Å

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Processing

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

3hzw


Resolution: 1.48→45.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.304 / SU ML: 0.051 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22294 1138 5.1 %RANDOM
Rwork0.20646 ---
obs0.20732 22198 88.27 %-
all-22361 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.884 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.48→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 14 351 1317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022985
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1772.0171308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6325111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2623.94738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67415187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.54155
X-RAY DIFFRACTIONr_chiral_restr0.0970.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02696
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3410.2775
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.2673
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2356
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.261
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8171.5607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2532935
X-RAY DIFFRACTIONr_scbond_it1.7283401
X-RAY DIFFRACTIONr_scangle_it2.6654.5373
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 82 -
Rwork0.394 1533 -
obs--88.25 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1proteinprotein
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3isopropanolisopropanol

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