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- PDB-6tmy: Crystal structure of isoform CBd of the basic phospholipase A2 su... -

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Basic information

Entry
Database: PDB / ID: 6tmy
TitleCrystal structure of isoform CBd of the basic phospholipase A2 subunit of crotoxin from Crotalus durissus terrificus
ComponentsPhospholipase A2 crotoxin basic subunit CBc
KeywordsHYDROLASE / crotoxin / CB isoforms / presynaptic phospholipase A2
Function / homology
Function and homology information


venom-mediated edema / venom-mediated muscle damage in another organism / venom-mediated myocyte killing in another organism / venom-mediated platelet aggregation / ion channel regulator activity / phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation ...venom-mediated edema / venom-mediated muscle damage in another organism / venom-mediated myocyte killing in another organism / venom-mediated platelet aggregation / ion channel regulator activity / phospholipase A2 / 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 domain superfamily
Similarity search - Domain/homology
Phospholipase A2 crotoxin basic subunit CBc
Similarity search - Component
Biological speciesCrotalus durissus terrificus (tropical rattlesnake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNemecz, D. / Ostrowski, M. / Saul, F.A. / Faure, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Other governmentPOKL.04.01.01-00-081/10 Poland
CitationJournal: Molecules / Year: 2020
Title: Crystal Structure of Isoform CBd of the Basic Phospholipase A 2 Subunit of Crotoxin: Description of the Structural Framework of CB for Interaction with Protein Targets.
Authors: Nemecz, D. / Ostrowski, M. / Ravatin, M. / Saul, F. / Faure, G.
History
DepositionDec 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Jan 24, 2024Group: 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 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 crotoxin basic subunit CBc
B: Phospholipase A2 crotoxin basic subunit CBc
C: Phospholipase A2 crotoxin basic subunit CBc
D: Phospholipase A2 crotoxin basic subunit CBc
E: Phospholipase A2 crotoxin basic subunit CBc
F: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,73238
Polymers85,6836
Non-polymers3,04932
Water14,628812
1
A: Phospholipase A2 crotoxin basic subunit CBc
B: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules

E: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules

C: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,23126
Polymers57,1224
Non-polymers2,10922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation4_557-x+1/2,y+1/2,-z+21
Buried area9730 Å2
ΔGint-129 kcal/mol
Surface area23920 Å2
MethodPISA
2
F: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules

F: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules

D: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules

D: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,00124
Polymers57,1224
Non-polymers1,88020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_558-x+1/2,y+1/2,-z+31
Buried area9070 Å2
ΔGint-125 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.626, 75.592, 109.012
Angle α, β, γ (deg.)90.000, 121.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-317-

HOH

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Components

#1: Protein
Phospholipase A2 crotoxin basic subunit CBc / svPLA2 / Phosphatidylcholine 2-acylhydrolase


Mass: 14280.483 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Crotalus durissus terrificus (tropical rattlesnake)
References: UniProt: P62022, phospholipase A2
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400, 0.1M NACL, 0.18M SODIUM ACETATE, 0.1M TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→47.5 Å / Num. obs: 94489 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 33.29 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4708 / % possible all: 97

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R0L POLYPEPTIDE CHAIN D

3r0l


Resolution: 1.8→47.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1857 1.97 %RANDOM
Rwork0.192 ---
obs0.192 94480 98.7 %-
Displacement parametersBiso max: 125.64 Å2 / Biso mean: 37.38 Å2 / Biso min: 16.73 Å2
Baniso -1Baniso -2Baniso -3
1-4.169 Å20 Å2-4.76 Å2
2--0.3929 Å20 Å2
3----4.5619 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.8→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5879 0 149 812 6840
Biso mean--52.39 45.25 -
Num. residues----732
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2154SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1019HARMONIC5
X-RAY DIFFRACTIONt_it6221HARMONIC20
X-RAY DIFFRACTIONt_nbd9SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion739SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7444SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6221HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8351HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion14.72
LS refinement shellResolution: 1.8→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.35 28 1.48 %
Rwork0.2609 1862 -
all0.2623 1890 -
obs--96.35 %

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