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- PDB-1sv3: Structure of the complex formed between Phospholipase A2 and 4-me... -

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Basic information

Entry
Database: PDB / ID: 1sv3
TitleStructure of the complex formed between Phospholipase A2 and 4-methoxybenzoic acid at 1.3A resolution.
ComponentsPhospholipase A2
KeywordsHYDROLASE / Phospholipase A2 / complex / 4-methoxybenzoic acid / 1.3A resolution
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
4-METHOXYBENZOIC ACID / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSingh, N. / Prahathees, E. / Jabeen, T. / Pal, A. / Ethayathulla, A.S. / Prem kumar, R. / Sharma, S. / 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
DepositionMar 27, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2627
Polymers13,6301
Non-polymers6326
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.570, 52.570, 47.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological Unit is Monomer

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Components

#1: Protein Phospholipase A2 / Phospholipase A2 / Phosphatidylcholine 2- acylhydrolase


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2M Ammonium sulphate, 50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 203 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.803
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 29, 2003 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 28771 / Num. obs: 28771 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.119 / Net I/σ(I): 8.8
Reflection shellResolution: 1.3→1.36 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.42 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FB2

1fb2


Resolution: 1.35→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.651 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24267 1364 5.1 %RANDOM
Rwork0.20822 ---
all0.2147 28771 --
obs0.20986 25474 93.28 %-
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: 20.353 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refine analyzeLuzzati coordinate error obs: 0.1971 Å
Refinement stepCycle: LAST / Resolution: 1.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 36 209 1189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021992
X-RAY DIFFRACTIONr_bond_other_d0.0010.02823
X-RAY DIFFRACTIONr_angle_refined_deg1.7812.0221327
X-RAY DIFFRACTIONr_angle_other_deg0.90631941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4173113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63215181
X-RAY DIFFRACTIONr_chiral_restr0.0960.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021035
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02195
X-RAY DIFFRACTIONr_nbd_refined0.4380.3283
X-RAY DIFFRACTIONr_nbd_other0.210.3849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.5151
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1560.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1760.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.522
X-RAY DIFFRACTIONr_mcbond_it1.0321.5592
X-RAY DIFFRACTIONr_mcangle_it1.7712934
X-RAY DIFFRACTIONr_scbond_it2.153400
X-RAY DIFFRACTIONr_scangle_it3.1124.5393
LS refinement shellResolution: 1.349→1.384 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 104
Rwork0.283 1928

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