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- PDB-1jq8: Design of specific inhibitors of phospholipase A2: Crystal struct... -

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Basic information

Entry
Database: PDB / ID: 1jq8
TitleDesign of specific inhibitors of phospholipase A2: Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Leu-Ala-Ile-Tyr-Ser at 2.0 resolution
Components
  • Peptide inhibitor
  • Phospholipase A2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / neurotoxic / designed peptide / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR 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
ACETIC ACID / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Betzel, C. / Singh, T.P.
Citation
Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2002
Title: Design of specific peptide inhibitors of phospholipase A2: structure of a complex formed between Russell's viper phospholipase A2 and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS).
Authors: Chandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Srinivasan, A. / Betzel, C.h. / Singh, T.P.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from Daboia russelli pulchella at 2.4 resolution
Authors: Chandra, V. / Kaur, P. / Srinivasan, A. / Singh, T.P.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Regulation of catalytic function by molecular association: structure of phospholipase A2 from Daboia russelli pulchella (DPLA2) at 1.9 A resolution
Authors: Chandra, V. / Kaur, P. / Jasti, J. / Betzel, C. / Singh, T.P.
#3: Journal: J.Mol.Biol. / Year: 2002
Title: First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between ...Title: First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between phospholipase A2 and alpha-tocopherol at 1.8 A resolution
Authors: Chandra, V. / Jasti, J. / Kaur, P. / Betzel, C. / Srinivasan, A. / Singh, T.P.
#4: Journal: Biochemistry / Year: 2002
Title: Structural basis of phospholipase A2 inhibition for the synthesis of prostaglandins by the plant alkaloid aristolochic acid from a 1.7 A crystal structure
Authors: Chandra, V. / Jasti, J. / Kaur, P. / Srinivasan, A. / Betzel, C. / Singh, T.P.
History
DepositionAug 4, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Oct 23, 2019Group: Data collection / Category: diffrn_source / reflns_shell
Item: _diffrn_source.pdbx_synchrotron_site / _reflns_shell.Rmerge_I_obs
Revision 1.6Oct 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2
B: Phospholipase A2
P: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1017
Polymers27,8253
Non-polymers2764
Water5,098283
1
A: Phospholipase A2
P: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3524
Polymers14,1952
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-20 kcal/mol
Surface area6980 Å2
MethodPISA
2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7503
Polymers13,6301
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.825, 90.375, 77.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

21B-331-

HOH

31B-333-

HOH

41B-355-

HOH

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Components

#1: Protein Phospholipase A2 /


Mass: 13629.767 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / References: UniProt: P59071*PLUS, phospholipase A2
#2: Protein/peptide Peptide inhibitor


Mass: 565.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the sequence was Chemically synthesized.
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE COMPLETE SEQUENCE FOR THIS STRUCTURE IS 121 RESIDUES LONG. GENBANK AAB47213 (ACCESSION 1839639) ...THE COMPLETE SEQUENCE FOR THIS STRUCTURE IS 121 RESIDUES LONG. GENBANK AAB47213 (ACCESSION 1839639) MATCHED EXACTLY WITH THE FIRST 50 RESIDUES OF THIS STRUCTURE. AN ADEQUATE DATABASE MATCH COULD NOT BE FOUND FOR THE COMPLETE 121 RESIDUE SEQUENCE. THE COMPLETE SEQUENCE IS PRESENT IN THE REFERENCE PAPER: GOWDA ET AL., TOXICON 32 (6) 665-673 (1994).

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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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 mM1dropCaCl2
23 %dioxane1drop
320 mg/mlsodium cacodylate1droppH6.5
415 mg/mlprotein1drop
51.4 Mammonium sulfate1reservoir
63 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 17914 / Num. obs: 17914 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.02 / Net I/σ(I): 9.22
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 4.3 / Mean I/σ(I) obs: 9.4 / Num. unique all: 1605 / Rsym value: 0.17 / % possible all: 90.3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. measured all: 222133 / Rmerge(I) obs: 0.02
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 88.1 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 1FE7

1fe7
PDB Unreleased entry


Resolution: 2→11.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1312150.02 / Data cutoff high rms absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 861 4.8 %RANDOM
Rwork0.187 ---
all0.189 17841 --
obs0.187 17841 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.4746 Å2 / ksol: 0.306488 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---1.13 Å20 Å2
3---0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→11.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 17 283 2228
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.032
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.081.5
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scbond_it3.542
X-RAY DIFFRACTIONc_scangle_it4.772.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.202 143 5.1 %
Rwork0.202 2684 -
obs-1605 92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CAR.PARAMCAR.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection obs: 17914 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.71

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