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- PDB-1fe5: SEQUENCE AND CRYSTAL STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM C... -

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Basic information

Entry
Database: PDB / ID: 1fe5
TitleSEQUENCE AND CRYSTAL STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM COMMON KRAIT (BUNGARUS CAERULEUS) AT 2.4 RESOLUTION: IDENTIFICATION AND CHARACTERIZATION OF ITS PHARMACOLOGICAL SITES.
ComponentsPHOSPHOLIPASE A2
KeywordsTOXIN / Bungarus caeruleus / phospholipase A2 (PLA2) / presynaptic neurotoxin / neurotoxic site / X-ray structure / molecular replacement
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic 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, 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 KPA2
Similarity search - Component
Biological speciesBungarus caeruleus (cobra)
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsSingh, G. / Gourinath, S. / Sharma, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Sequence and crystal structure determination of a basic phospholipase A2 from common krait (Bungarus caeruleus) at 2.4 A resolution: identification and characterization of its pharmacological sites.
Authors: Singh, G. / Gourinath, S. / Sharma, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P.
History
DepositionJul 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0312
Polymers12,9901
Non-polymers401
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.980, 57.980, 57.980
Angle α, β, γ (deg.)92.02, 92.02, 92.02
Int Tables number155
Space group name H-MR32
DetailsPhospholipase A2 monomer in each assymetric unit

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 12990.490 Da / Num. of mol.: 1 / Fragment: NATURAL PROTEIN / Source method: isolated from a natural source / Source: (natural) Bungarus caeruleus (cobra) / Secretion: VENOM / References: UniProt: Q9DF52, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: Ammonium sulphate, CaCl2, Dioxane, Sodium cacodylate , pH 7.0, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1drop
31.4 M1dropNaCl
41 mM1dropNaN3
53.5 M1reservoirNaN3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→15 Å / Num. all: 79758 / Num. obs: 4629 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 7.2
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.223 / Num. unique all: 521 / % possible all: 70.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.9 Å / % possible obs: 92 % / Rmerge(I) obs: 0.174

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.45→9.99 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 151511.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 356 7.9 %RANDOM
Rwork0.201 ---
all0.217 4629 --
obs0.201 4535 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.46 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å23.59 Å23.59 Å2
2--0 Å23.59 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.45→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms897 0 1 77 975
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it2.742
X-RAY DIFFRACTIONc_scbond_it3.062
X-RAY DIFFRACTIONc_scangle_it4.522.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 45 8 %
Rwork0.327 521 -
obs--70.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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