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

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Basic information

Entry
Database: PDB / ID: 3hzw
TitleCrystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB)
ComponentsPhospholipase A2 homolog bothropstoxin-1
KeywordsTOXIN / Lys49-PLA2 / Phospholipase homologue / myotoxicity / p-bromophenacyl bromide / Bothropstoxin-I / Antibiotic / Antimicrobial / Disulfide bond / Myotoxin / Secreted
Function / homology
Function and homology information


: / 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, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain / Phospholipase A2 ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain / Phospholipase A2 / 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: 2.28 Å
AuthorsFernandes, C.A.H. / 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 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 1.4Jul 4, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_validate_close_contact / struct_conn
Revision 2.0Nov 27, 2019Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)28,1225
Polymers27,5062
Non-polymers6163
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-11.9 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.670, 62.460, 87.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C8H6Br2O
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% w/v PEG 4000, 20% w/v Isopropanol, 0.1 M 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: 1.425 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 14, 2006
RadiationMonochromator: 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: 2.28→50.77 Å / Num. all: 12419 / Num. obs: 11778 / % possible obs: 94.8 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.28→2.36 Å / % possible all: 94.8

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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 3HZD

3hzd


Resolution: 2.28→50.77 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25445 612 4.9 %RANDOM
Rwork0.23515 ---
obs0.23605 11778 94.31 %-
all-11778 --
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: 48.739 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20 Å2
2---0.61 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.28→50.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 24 127 2024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0221945
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.1782.0112612
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.875236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.25724.15677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.08615351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3751510
X-RAY DIFFRACTIONr_chiral_restr0.1220.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0420.021449
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3350.21293
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3380.21344
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.411.51191
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43521887
X-RAY DIFFRACTIONr_scbond_it1.9663754
X-RAY DIFFRACTIONr_scangle_it2.994.5725
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 45 -
Rwork0.337 846 -
obs--93.4 %

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