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- PDB-3t0r: Crystal Structure of MjTX-I, a myotoxic Lys49-phospholipase A2 fr... -

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Basic information

Entry
Database: PDB / ID: 3t0r
TitleCrystal Structure of MjTX-I, a myotoxic Lys49-phospholipase A2 from Bothrops moojeni
ComponentsPhospholipase A2 homolog 1
KeywordsTOXIN / Lys49-phospholipase A2 / Myotoxin / Venom Glands
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / phospholipid binding / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 homolog MjTX-I
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsSalvador, G.H.M. / Marchi-Salvador, D.P. / Fontes, M.R.M.
CitationJournal: To be Published
Title: Crystal Structure of MjTX-I, a myotoxic Lys49-phospholipase A2 from Bothrops moojeni
Authors: Salvador, G.H.M. / Marchi-Salvador, D.P. / Fontes, M.R.M.
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Sep 13, 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
Revision 1.3Nov 27, 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: Phospholipase A2 homolog 1
B: Phospholipase A2 homolog 1
C: Phospholipase A2 homolog 1
D: Phospholipase A2 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4115
Polymers55,0564
Non-polymers3541
Water2,036113
1
A: Phospholipase A2 homolog 1
B: Phospholipase A2 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8833
Polymers27,5282
Non-polymers3541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Phospholipase A2 homolog 1
D: Phospholipase A2 homolog 1


Theoretical massNumber of molelcules
Total (without water)27,5282
Polymers27,5282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Phospholipase A2 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1192
Polymers13,7641
Non-polymers3541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Phospholipase A2 homolog 1


Theoretical massNumber of molelcules
Total (without water)13,7641
Polymers13,7641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Phospholipase A2 homolog 1


Theoretical massNumber of molelcules
Total (without water)13,7641
Polymers13,7641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Phospholipase A2 homolog 1


Theoretical massNumber of molelcules
Total (without water)13,7641
Polymers13,7641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.593, 125.848, 65.327
Angle α, β, γ (deg.)90.00, 105.91, 90.00
Int Tables number5
Space group name H-MC121
DetailsAccording to Small Angle X-ray Scattering experiments

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Components

#1: Protein
Phospholipase A2 homolog 1 / MjTX-I / Myotoxin I


Mass: 13764.075 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bothrops moojeni (Brazilian lancehead) / References: UniProt: P82114, phospholipase A2
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 32% (w/v) PEG 4000; 0.1 M Tris HCl; 0.15 M Magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
PH range: 8,5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.421 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 20, 2010 / Details: Mirrors
RadiationMonochromator: Si curved crystal asymmetrically-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.421 Å / Relative weight: 1
ReflectionResolution: 2.49→33.44 Å / Num. all: 15300 / Num. obs: 15300 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 43.016 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.64
Reflection shellResolution: 2.49→2.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.69 / Num. unique all: 1541 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLL

1qll


Resolution: 2.49→33.44 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.897 / SU B: 26.875 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26671 759 5 %RANDOM
Rwork0.23123 ---
obs0.23297 14529 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.016 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.05 Å2
2--0.05 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.49→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 24 113 3684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223654
X-RAY DIFFRACTIONr_angle_refined_deg2.1511.9764930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7595469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34724.228149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.06115609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3631523
X-RAY DIFFRACTIONr_chiral_restr0.1350.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212724
X-RAY DIFFRACTIONr_mcbond_it2.1531.52349
X-RAY DIFFRACTIONr_mcangle_it3.86723708
X-RAY DIFFRACTIONr_scbond_it4.54531305
X-RAY DIFFRACTIONr_scangle_it6.9534.51222
X-RAY DIFFRACTIONr_rigid_bond_restr2.59933654
LS refinement shellResolution: 2.49→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 54 -
Rwork0.3 1010 -
obs--92.84 %
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)
10.87610.54920.57242.09070.86370.5244-0.074-0.03930.09650.03970.0596-0.1054-0.0384-0.02120.01450.08540.02340.0090.13820.01910.156936.111963.314132.7092
20.3150.8960.26583.44060.12161.09690.03470.081-0.09940.27220.112-0.19780.014-0.0273-0.14670.0657-0.00950.03650.16660.05230.191433.102731.437828.2515
30.846-0.4488-0.06294.11010.85232.8526-0.0735-0.08250.1065-0.01370.28330.06070.12450.104-0.20980.09980.1018-0.02360.1497-0.00880.084316.787477.31530.7287
41.0233-0.47250.54354.30311.27922.4087-0.1879-0.1217-0.17660.7840.43780.13740.0783-0.2436-0.24980.25040.1510.0960.20120.12240.096216.849146.0666-2.0331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 133
2X-RAY DIFFRACTION2B1 - 133
3X-RAY DIFFRACTION3C1 - 133
4X-RAY DIFFRACTION4D1 - 133

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