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- PDB-1tj9: Structure of the complexed formed between group II phospholipase ... -

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Basic information

Entry
Database: PDB / ID: 1tj9
TitleStructure of the complexed formed between group II phospholipase A2 and a rationally designed tetra peptide,Val-Ala-Arg-Ser at 1.1A resolution
Components
  • Phospholipase A2
  • VARS peptide
KeywordsHYDROLASE / PHOSPHOLIPASE / COMPLEX / VARS / 1.1 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
ACETIC ACID / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii russellii (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsSingh, N. / Ethayathulla, A.S. / K Somvanshi, R. / Sharma, S. / Dey, S. / Perbandt, M. / Betzel, C. / Kaur, P. / Singh, T.P.
CitationJournal: TO BE PUBLISHED
Title: Structure of the complex formed between group II phospholipase A2 and a rationally designed tetra peptide,Val-Ala-Arg-Ser at 1.1A resolution
Authors: Singh, N. / Ethayathulla, A.S. / K Somvanshi, R. / Sharma, S. / Dey, S. / Perbandt, M. / Betzel, C. / Kaur, P. / Singh, T.P.
History
DepositionJun 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Aug 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2
B: VARS peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6038
Polymers14,0622
Non-polymers5406
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.513, 52.513, 48.037
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: snake venom / References: UniProt: P59071, phospholipase A2
#2: Protein/peptide VARS peptide


Mass: 432.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: VARS-solid phase peptide synthesis
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M AMMONIUM SULPHATE, 30% PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.806 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 2, 2004 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.806 Å / Relative weight: 1
ReflectionResolution: 1.1→52 Å / Num. all: 53031 / Num. obs: 53031 / % possible obs: 100 % / Redundancy: 15.3 % / Biso Wilson estimate: 11 Å2 / Rsym value: 0.071 / Net I/σ(I): 22.5
Reflection shellResolution: 1.1→1.12 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.522 / % possible all: 100

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Processing

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

1skg


Resolution: 1.1→52 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.602 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20896 1088 2.1 %RANDOM
Rwork0.18665 ---
all0.188 53031 --
obs0.18707 51861 99.85 %-
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: 13.218 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.1→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 29 212 1215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211016
X-RAY DIFFRACTIONr_bond_other_d0.0010.02855
X-RAY DIFFRACTIONr_angle_refined_deg1.6462.0151356
X-RAY DIFFRACTIONr_angle_other_deg0.70732015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3663116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64315192
X-RAY DIFFRACTIONr_chiral_restr0.0870.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021059
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02198
X-RAY DIFFRACTIONr_nbd_refined0.4410.3280
X-RAY DIFFRACTIONr_nbd_other0.2230.3863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.5136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.330
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.524
X-RAY DIFFRACTIONr_mcbond_it0.8411.5615
X-RAY DIFFRACTIONr_mcangle_it1.4712966
X-RAY DIFFRACTIONr_scbond_it1.6823401
X-RAY DIFFRACTIONr_scangle_it2.5484.5390
LS refinement shellResolution: 1.1→1.12 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.258 92
Rwork0.254 3816

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