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- PDB-2h8i: Crystal Structure of the Bothropstoxin-I complexed with polyethyl... -

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Basic information

Entry
Database: PDB / ID: 2h8i
TitleCrystal Structure of the Bothropstoxin-I complexed with polyethylene glycol
ComponentsPhospholipase A2 homolog 1
KeywordsTOXIN / Lys49-PLA2s / myotoxicity
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
DI(HYDROXYETHYL)ETHER / Basic phospholipase A2 homolog bothropstoxin-I
Similarity search - Component
Biological speciesBothrops jararacussu (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMurakami, M.T. / Arni, R.K.
CitationJournal: Toxicon / Year: 2007
Title: Interfacial surface charge and free accessibility to the PLA2-active site-like region are essential requirements for the activity of Lys49 PLA2 homologues
Authors: Murakami, M.T. / Vicotia, M.M. / Abrego, J.R.B. / Lourenzoni, M.R. / Cintra, A.C.O. / Arruda, E.Z. / Tomaz, M.A. / Melo, P.A. / Arni, R.K.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The 21th residue is TYR and is a variant present in nature. The 58th and 120th residues ...sequence The 21th residue is TYR and is a variant present in nature. The 58th and 120th residues are ASN and PRO respectively according to Cintra A.C.O. et al.[J. Protein Chem. 12: 57-64(1993)].

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,7174
Polymers27,5042
Non-polymers2122
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-9 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.019, 56.019, 127.568
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is the dimer formed in the asymmetric unit.

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Components

#1: Protein Phospholipase A2 homolog 1 / Bothropstoxin I / BthTX-I / BtxtxI


Mass: 13752.150 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: venom gland / Source: (natural) Bothrops jararacussu (jararacussu) / References: UniProt: Q90249
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 400, 2M ammonium sulphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.438 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.438 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 21766 / Num. obs: 18722 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.053
Reflection shellResolution: 1.9→1.94 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
DENZOdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.37 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27688 964 5.1 %RANDOM
Rwork0.22504 ---
all0.262 18722 --
obs0.22757 17758 99.6 %-
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: 41.481 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 14 122 2038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221972
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.9922639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.025240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2623.84678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.10715376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.061510
X-RAY DIFFRACTIONr_chiral_restr0.2020.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021434
X-RAY DIFFRACTIONr_nbd_refined0.2510.21214
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.210
X-RAY DIFFRACTIONr_mcbond_it1.1481.51233
X-RAY DIFFRACTIONr_mcangle_it1.85921914
X-RAY DIFFRACTIONr_scbond_it2.8213854
X-RAY DIFFRACTIONr_scangle_it4.1074.5725
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 93 -
Rwork0.247 1203 -
obs--98.63 %
Refinement TLS params.Method: refined / Origin x: 0.7898 Å / Origin y: 23.3794 Å / Origin z: 52.1856 Å
111213212223313233
T-0.0619 Å20.0181 Å2-0.0754 Å2--0.0115 Å2-0.0223 Å2---0.0595 Å2
L0.9445 °2-1.1384 °2-0.7164 °2-1.9748 °20.5471 °2--0.7096 °2
S-0.0393 Å °0.0369 Å °0.0479 Å °0.1744 Å °0.0007 Å °-0.1516 Å °0.0505 Å °-0.0639 Å °0.0386 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1211 - 121
2X-RAY DIFFRACTION1BB1 - 1211 - 121

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