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- PDB-7rox: BthTX-I complexed with inhibitor MMV -

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Basic information

Entry
Database: PDB / ID: 7rox
TitleBthTX-I complexed with inhibitor MMV
ComponentsBasic phospholipase A2 homolog bothropstoxin-I
KeywordsTOXIN / BthTX-I / phospholipase A2-like protein / 12-methoxy-4-methylvoachalotine (MMV) / Tabernaemontana catharinensis / Bothrops jararacussu
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 domain superfamily
Similarity search - Domain/homology
12-methoxy-Nb-methylvoachalotine / Basic phospholipase A2 homolog bothropstoxin-I
Similarity search - Component
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBorges, R.J. / De Marino, I. / Uson, I. / Fontes, M.R.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)16/24191-8 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)302883/2017-7 Brazil
CitationJournal: Biochimie / Year: 2023
Title: Structural and functional studies of a snake venom phospholipase A 2 -like protein complexed to an inhibitor from Tabernaemontana catharinensis.
Authors: Borges, R.J. / Cardoso, F.F. / de Carvalho, C. / de Marino, I. / Pereira, P.S. / Soares, A.M. / Dal-Pai-Silva, M. / Uson, I. / Fontes, M.R.M.
History
DepositionAug 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basic phospholipase A2 homolog bothropstoxin-I
B: Basic phospholipase A2 homolog bothropstoxin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9183
Polymers27,5062
Non-polymers4121
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-7 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.920, 104.920, 64.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-256-

HOH

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Components

#1: Protein Basic phospholipase A2 homolog bothropstoxin-I / Bothropstoxin I / BthTx-I / BtxtxI / svPLA2 homolog / BOJU-I / Myotoxic phospholipase A2-like / ...Bothropstoxin I / BthTx-I / BtxtxI / svPLA2 homolog / BOJU-I / Myotoxic phospholipase A2-like / Phospholipase A2 homolog 1


Mass: 13753.136 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops jararacussu (jararacussu) / References: UniProt: Q90249, phospholipase A2
#2: Chemical ChemComp-85O / 12-methoxy-Nb-methylvoachalotine


Mass: 411.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H31N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.76 Å3/Da / Density % sol: 67.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate, pH 5.6, 20% PEG4000, 22% isopropanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.439 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.439 Å / Relative weight: 1
ReflectionResolution: 2.1→26.28 Å / Num. obs: 24142 / % possible obs: 99.8 % / Redundancy: 9.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.039 / Rrim(I) all: 0.121 / Χ2: 0.99 / Net I/σ(I): 17.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 7.9 / Num. unique obs: 1959 / CC1/2: 0.313 / Rpim(I) all: 0.12 / Rrim(I) all: 0.354 / Χ2: 1.34 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLM7.3.0data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
Coot0.9.5model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wtb

4wtb


Resolution: 2.1→26.23 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 17.9 / Phase error: 18.55 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1984 1227 5.09 %
Rwork0.1672 --
obs0.179 24101 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→26.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 30 238 2078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041877
X-RAY DIFFRACTIONf_angle_d0.782532
X-RAY DIFFRACTIONf_dihedral_angle_d18.418283
X-RAY DIFFRACTIONf_chiral_restr0.042262
X-RAY DIFFRACTIONf_plane_restr0.004325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.29071180.23472510X-RAY DIFFRACTION95
2.18-2.280.21191380.20682508X-RAY DIFFRACTION94
2.28-2.40.25551150.19192508X-RAY DIFFRACTION95
2.4-2.550.21821480.1852533X-RAY DIFFRACTION94
2.55-2.750.19591420.18012517X-RAY DIFFRACTION95
2.75-3.030.20111560.1662523X-RAY DIFFRACTION94
3.03-3.460.18091280.16332545X-RAY DIFFRACTION95
3.47-4.360.20461300.15842607X-RAY DIFFRACTION95
4.36-26.230.19341510.17292624X-RAY DIFFRACTION94

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