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- PDB-2arm: Crystal Structure of the Complex of Phospholipase A2 with a natur... -

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Basic information

Entry
Database: PDB / ID: 2arm
TitleCrystal Structure of the Complex of Phospholipase A2 with a natural compound atropine at 1.2 A resolution
ComponentsPhospholipase A2 VRV-PL-VIIIa
KeywordsHYDROLASE / Enzyme / complex
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic 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, 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
Chem-OIN / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsSingh, N. / Pal, A. / Jabeen, T. / Sharma, S. / Perbandt, M. / Betzel, C. / Singh, T.P.
CitationJournal: Proteins / Year: 2006
Title: Crystal structures of the complexes of a group IIA phospholipase A2 with two natural anti-inflammatory agents, anisic acid, and atropine reveal a similar mode of binding
Authors: Singh, N. / Jabeen, T. / Pal, A. / Sharma, S. / Perbandt, M. / Betzel, C. / Singh, T.P.
History
DepositionAug 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3036
Polymers13,6301
Non-polymers6745
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.350, 52.350, 47.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Phospholipase A2 VRV-PL-VIIIa / Phosphatidylcholine 2-acylhydrolase / DPLA2


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / References: UniProt: P59071, phospholipase A2
#2: Chemical ChemComp-OIN / (1R,5S)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL (2R)-3-HYDROXY-2-PHENYLPROPANOATE / ATROPINE / Atropine


Mass: 289.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23NO3 / Comment: medication, alkaloid*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ammonium sulphate and PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2004 / Details: Mirorr
RadiationMonochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.23→51.99 Å / Num. all: 36667 / Num. obs: 36667 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.23→1.26 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→51.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.879 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20444 767 2 %RANDOM
Rwork0.18877 ---
all0.2 36667 --
obs0.18909 36667 99.82 %-
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: 14.146 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.23→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 41 247 1231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021998
X-RAY DIFFRACTIONr_bond_other_d0.0010.02832
X-RAY DIFFRACTIONr_angle_refined_deg1.9462.0281336
X-RAY DIFFRACTIONr_angle_other_deg0.7931965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9753113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.45115181
X-RAY DIFFRACTIONr_chiral_restr0.2110.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021032
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02196
X-RAY DIFFRACTIONr_nbd_refined0.4350.3299
X-RAY DIFFRACTIONr_nbd_other0.2130.3819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.5161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.539
X-RAY DIFFRACTIONr_mcbond_it0.6351.5594
X-RAY DIFFRACTIONr_mcangle_it1.1912937
X-RAY DIFFRACTIONr_scbond_it1.3993404
X-RAY DIFFRACTIONr_scangle_it2.1644.5399
LS refinement shellResolution: 1.233→1.265 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 55
Rwork0.264 2663

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