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- PDB-1rgb: Phospholipase A2 from Vipera ammodytes meridionalis -

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Basic information

Entry
Database: PDB / ID: 1rgb
TitlePhospholipase A2 from Vipera ammodytes meridionalis
ComponentsPhospholipase A2
KeywordsHYDROLASE / Phospholipase A2 / Neurotoxin / Elaidoylamide
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / killing of cells of another organism / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(9E)-OCTADEC-9-ENAMIDE / Basic phospholipase A2 vipoxin B chain
Similarity search - Component
Biological speciesVipera ammodytes meridionalis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGeorgieva, D.N.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Asp49 phospholipase A(2)-elaidoylamide complex: a new mode of inhibition.
Authors: Georgieva, D.N. / Rypniewski, W. / Gabdoulkhakov, A. / Genov, N. / Betzel, C.
History
DepositionNov 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2
B: Phospholipase A2
K: Phospholipase A2
L: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9506
Polymers55,3874
Non-polymers5632
Water0
1
A: Phospholipase A2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9753
Polymers27,6942
Non-polymers2811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-18 kcal/mol
Surface area11790 Å2
MethodPISA
2
K: Phospholipase A2
L: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9753
Polymers27,6942
Non-polymers2811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-18 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.568, 82.670, 119.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phospholipase A2 / / Phosphatidylcholine 2-acylhydrolase / Vipoxin non-toxic component / Vipoxin B chain


Mass: 13846.822 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Vipera ammodytes meridionalis (snake) / Secretion: venom / Species: Vipera ammodytes / Strain: meridionalis / References: UniProt: P14420, phospholipase A2
#2: Chemical ChemComp-ELD / (9E)-OCTADEC-9-ENAMIDE / ELAIDOYLAMIDE


Mass: 281.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H35NO

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG-8000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.3→19.53 Å / Num. obs: 6922

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→19.53 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 995111.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.286 349 5 %RANDOM
Rwork0.234 ---
obs0.234 6922 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.6522 Å2 / ksol: 0.125113 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 40 0 3892
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.411.5
X-RAY DIFFRACTIONc_mcangle_it5.622
X-RAY DIFFRACTIONc_scbond_it13.632
X-RAY DIFFRACTIONc_scangle_it16.232.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 64 5.9 %
Rwork0.309 1030 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2OLA1.PARAMOLA1.TOP

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