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- PDB-5tfv: Crystal Structure of MT-I isolated from Bothrops asper venom. -

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Basic information

Entry
Database: PDB / ID: 5tfv
TitleCrystal Structure of MT-I isolated from Bothrops asper venom.
ComponentsBasic phospholipase A2 myotoxin III
KeywordsTOXIN / Bothrops asper / myotoxin / myotoxic Asp49-PLA2
Function / homology
Function and homology information


phospholipase A2 activity / phospholipase A2 / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / 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
Basic phospholipase A2 myotoxin I
Similarity search - Component
Biological speciesBothrops asper (terciopelo)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsSalvador, G.H.M. / dos Santos, J.I. / Fontes, M.R.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: Biochimie / Year: 2017
Title: Crystal structure of a phospholipase A2 from Bothrops asper venom: Insights into a new putative "myotoxic cluster".
Authors: Salvador, G.H. / Dos Santos, J.I. / Lomonte, B. / Fontes, M.R.
History
DepositionSep 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basic phospholipase A2 myotoxin III
B: Basic phospholipase A2 myotoxin III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2234
Polymers27,9792
Non-polymers2442
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-6 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.534, 56.534, 136.459
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-201-

TRS

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Components

#1: Protein Basic phospholipase A2 myotoxin III / svPLA2 / Myotoxin I / Phosphatidylcholine 2-acylhydrolase


Mass: 13989.292 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops asper (terciopelo) / References: UniProt: P20474, phospholipase A2
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350 and 0.2 M triammonium citrate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.459 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 27, 2013
RadiationMonochromator: Single Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.54→33.32 Å / Num. obs: 8750 / % possible obs: 99.73 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.08 / Net I/av σ(I): 5.39 / Net I/σ(I): 20.31
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.7 / % possible all: 99.53

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3jr8

3jr8


Resolution: 2.54→33.32 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 444 5.08 %Random selection
Rwork0.2424 ---
obs0.2435 8746 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.54→33.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 16 34 1894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021916
X-RAY DIFFRACTIONf_angle_d0.6192572
X-RAY DIFFRACTIONf_dihedral_angle_d12.801694
X-RAY DIFFRACTIONf_chiral_restr0.026268
X-RAY DIFFRACTIONf_plane_restr0.003332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5477-2.91620.41481470.38742690X-RAY DIFFRACTION100
2.9162-3.67330.3351420.3092747X-RAY DIFFRACTION100
3.6733-33.32690.21451550.19412865X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.00960.0464-0.00860.1781-0.06740.02650.5553-0.4369-0.1802-0.4168-0.3368-0.00620.7534-0.05230.00180.52570.03-0.06560.75750.1270.5959-2.110611.994310.3532
21.04950.5868-1.01490.75010.32822.58950.2454-0.5957-0.24310.03980.0150.23471.19950.2285-0.2920.54380.0949-0.14310.94510.16520.62815.99388.190116.7154
31.015-0.4144-0.48630.6807-0.02863.41630.07920.1252-0.0958-0.0026-0.15960.48710.5027-0.0405-0.15720.3603-0.0433-0.08731.21810.13390.707-8.940613.196124.415
4-0.0047-0.0249-0.011.03880.61020.37960.70450.8824-0.7455-0.3755-0.69210.45840.1881-0.451-0.27110.4310.1532-0.121.01560.10690.5565-4.075320.95113.4566
50.62641.4636-0.69243.3194-1.59240.79310.4247-0.50450.43941.02220.0024-0.4394-0.41990.2832-0.03410.52320.17870.02210.95090.00120.74521.562931.856212.7782
60.0164-0.0302-0.02790.28210.29560.30860.28880.0532-0.28740.0222-0.34040.1967-0.4472-0.659-0.04760.57650.1045-0.03950.84350.19440.7743-6.475634.82649.2206
70.02960.01780.01090.06160.05270.07720.1654-0.1437-0.38210.22160.0458-0.0737-0.2374-0.13150.00230.40220.0913-0.00640.8070.02880.7823-20.595532.320811.8672
80.04820.06850.01770.13260.08140.0992-0.5693-0.1176-0.03860.4023-0.2057-0.104-0.3415-0.3104-0.00250.5992-0.0203-0.14891.26730.08690.9307-17.454223.27510.3857
90.03860.0647-0.00920.10560.09090.22250.52821.01880.1551-0.4211-0.4419-0.4060.56480.0749-0.0030.59950.33070.00461.3502-0.09950.7218-13.320523.807-5.5049
100.16720.39410.02881.52760.39440.16420.0762-0.12420.35390.1713-0.37940.57060.03520.01960.02241.08970.1877-0.18551.7147-0.09770.9792-20.66326.8151-2.1169
11-0.0008-0.00930.01430.1788-0.07560.04440.1758-0.40920.31720.2312-0.2978-0.2956-0.5364-0.17890.02020.43650.16580.01720.98380.10320.6476-12.656130.05382.2756
120.3232-0.044-0.0036-0.0016-0.02350.0618-0.06230.09050.0755-0.15220.0898-0.2639-0.17060.00220.2494-0.14230.57810.01991.02920.51190.7927.856329.96154.126
130.05120.00190.04270.01450.01030.0258-0.3286-0.38070.1889-0.1579-0.17970.223-0.71350.9639-0.00150.84250.2224-0.01391.39460.12120.69833.452834.692518.115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 133 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 21 )
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 40 )
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 54 )
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 67 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 72 )
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 82 )
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 88 )
11X-RAY DIFFRACTION11chain 'B' and (resid 90 through 107 )
12X-RAY DIFFRACTION12chain 'B' and (resid 108 through 117 )
13X-RAY DIFFRACTION13chain 'B' and (resid 118 through 133 )

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