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- PDB-1th6: Crystal structure of phospholipase A2 in complex with atropine at... -

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Basic information

Entry
Database: PDB / ID: 1th6
TitleCrystal structure of phospholipase A2 in complex with atropine at 1.23A resolution
ComponentsPhospholipase A2
KeywordsHYDROLASE / Phospholipids / eicosanoids / inhibition
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / 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 russellii (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: To be Published
Title: Crystal structure of phospholipase A2 in complex with atropine at 1.23A resolution
Authors: Singh, N. / Pal, A. / Jabeen, T. / Sharma, S. / Perbandt, M. / Betzel, C. / Singh, T.P.
History
DepositionJun 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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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)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)52.331, 52.331, 48.071
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 / / Phosphatidylcholine 2-acylhydrolase / DPLA2


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii russellii (snake) / Species: Daboia russellii / Strain: russellii / Tissue: venom secretion / 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: 47.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M ammonium sulphate, 30% 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: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 19, 2004 / Details: Mirror
RadiationMonochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 1.23→51.99 Å / Num. all: 37504 / Num. obs: 37504 / % possible obs: 99.82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.053 / Net I/σ(I): 33.2
Reflection shellResolution: 1.23→1.25 Å / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SKG

1skg


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 ---
obs0.18909 36667 99.82 %-
all-37504 --
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: 1.23→1.265 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 55
Rwork0.264 2663

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