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- PDB-4eix: Structural Studies of the ternary complex of Phaspholipase A2 wit... -

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Basic information

Entry
Database: PDB / ID: 4eix
TitleStructural Studies of the ternary complex of Phaspholipase A2 with nimesulide and indomethacin
ComponentsPhospholipase A2 VRV-PL-VIIIa
KeywordsHYDROLASE
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate 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
ACETONITRILE / INDOMETHACIN / 4-NITRO-2-PHENOXYMETHANESULFONANILIDE / Basic phospholipase A2 VRV-PL-VIIIa / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShukla, P.K. / Singh, N. / Kumar, S. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Structural Studies of the ternary complex of Phaspholipase A2 with nimusulide and indomethacin
Authors: Shukla, P.K. / Singh, N. / Kumar, S. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 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 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3374
Polymers13,6301
Non-polymers7073
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.880, 52.880, 48.420
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


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake)
References: UniProt: D0VX11, UniProt: P59071*PLUS, phospholipase A2
#2: Chemical ChemComp-NIM / 4-NITRO-2-PHENOXYMETHANESULFONANILIDE / NIMESULIDE


Mass: 308.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N2O5S / Comment: medication, antiinflammatory*YM
#3: Chemical ChemComp-IMN / INDOMETHACIN


Mass: 357.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Comment: medication, antiinflammatory*YM
#4: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Ammonium Sulphate, PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2007 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→23.65 Å / Num. all: 2930 / Num. obs: 2930 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 42 Å2 / Rsym value: 0.181 / Net I/σ(I): 5.6
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.444 / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ARM

2arm


Resolution: 2.9→23.65 Å / Rfactor Rfree error: 0.018 / Occupancy max: 1 / Occupancy min: 0.8 / Data cutoff high absF: 617238.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 139 4.7 %RANDOM
Rwork0.184 ---
obs0.184 2930 96.2 %-
all-2930 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.701 Å2 / ksol: 0.339355 e/Å3
Displacement parametersBiso max: 78.41 Å2 / Biso mean: 28.6 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20 Å2
2--2.57 Å20 Å2
3----5.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.32 Å
Refinement stepCycle: LAST / Resolution: 2.9→23.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 49 44 1036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.192 25 5.6 %
Rwork0.254 420 -
obs--90.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION5ccn.paramccn.top

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