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- PDB-1fb2: STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT 1.95 -

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Basic information

Entry
Database: PDB / ID: 1fb2
TitleSTRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT 1.95
ComponentsPHOSPHOLIPASE A2
KeywordsTOXIN / Phospholipase A2 / Daboia Russelli Pulchella / Neurotoxic
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / phospholipid metabolic process / negative regulation of T cell proliferation / 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 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChandra, V. / Kaur, P. / Betzel, C. / Singh, T.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Regulation of catalytic function by molecular association: structure of phospholipase A2 from Daboia russelli pulchella (DPLA2) at 1.9 A resolution.
Authors: Chandra, V. / Kaur, P. / Jasti, J. / Betzel, C. / Singh, T.P.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Three-Dimensional Structure of a Presynaptic Neurotoxic Phospholipase A2 from Daboia Russelli pulchella at 2.4 Resolution
Authors: Chandra, V. / Kaur, P. / Srinivasan, A. / P Singh, T.
History
DepositionJul 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
B: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)27,2602
Polymers27,2602
Non-polymers00
Water3,837213
1
A: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,6301
Polymers13,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,6301
Polymers13,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.100, 88.050, 79.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Secretion: VENOM / Species: Daboia russellii / Strain: pulchella / Keywords: NATIVE / References: UniProt: P59071
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20mM Sodium Cacodylate, 1.4M Ammonium Sulphate, 4mM Calcium Chloride, 3% Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
220 mMsodium cacodylate1droppH6.5
31.4 Mammonium sulfate1reservoir
43 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→24.1 Å / Num. all: 19822 / Num. obs: 18001 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.026 / Net I/σ(I): 12.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 1913 / Rsym value: 0.165 / % possible all: 98.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 17922 / % possible obs: 91 % / Rmerge(I) obs: 0.026
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.163

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
PROLSQrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CL5

1cl5


Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used restrained least-squares refinement procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.272 863 4.8 %Random
Rwork0.216 ---
all0.234 17985 --
obs0.226 17922 90.9 %-
Displacement parametersBiso mean: 42.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 0 213 2101
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.3
X-RAY DIFFRACTIONp_bond_d0.006
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.3
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23

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