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- PDB-1jq9: Crystal structure of a complex formed between phospholipase A2 fr... -

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Basic information

Entry
Database: PDB / ID: 1jq9
TitleCrystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 resolution
Components
  • Peptide inhibitor
  • Phospholipase A2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / phospholipase A2 / Daboia russelli pulchella / 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: 1.8 Å
AuthorsChandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Betzel, C. / Singh, T.P.
Citation
Journal: J.BIOL.CHEM. / Year: 2002
Title: Crystal Structure of a Complex Formed between a Snake Venom Phospholipase A2 and a Potent Peptide Inhibitor Phe-Leu-Ser-Tyr-Lys at 1.8 A Resolution
Authors: Chandra, V. / Jasti, J. / Kaur, P. / Dey, S. / Perbandt, M. / Srinivasan, A. / Betzel, C. / 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.
#5: 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. / 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 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 23, 2019Group: Data collection / Category: diffrn_source / reflns_shell / struct_biol
Item: _diffrn_source.pdbx_synchrotron_site / _reflns_shell.Rmerge_I_obs
Revision 1.5Oct 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)28,1587
Polymers27,9173
Non-polymers2404
Water5,026279
1
A: Phospholipase A2
P: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4685
Polymers14,2882
Non-polymers1803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-7 kcal/mol
Surface area7030 Å2
MethodPISA
2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6902
Polymers13,6301
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-20 kcal/mol
Surface area12580 Å2
MethodPISA
4
B: Phospholipase A2
hetero molecules

A: Phospholipase A2
P: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1587
Polymers27,9173
Non-polymers2404
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-18 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.130, 89.161, 77.548
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
11B-372-

HOH

DetailsThe two protein chains (A and B) represent the two molecules in the asymmetric unit, with the A molecule containing peptide inhibitor

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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) / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2
#2: Protein/peptide Peptide inhibitor


Mass: 657.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE SEQUENCE WAS CHEMICALLY SYNTHESIZED.
#3: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
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
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlpeptide1drop
220 mMsodium cacodylate1droppH6.5
31.4 Mammonium sulfate1reservoir
43 %dioxane1reservoir
520 mMsodium cacodylate1reservoirpH6.5

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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: 1.8→20 Å / Num. all: 239988 / Num. obs: 239988 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.04 / Net I/σ(I): 9.44
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 4.7 / Mean I/σ(I) obs: 9.9 / Num. unique all: 1581 / Rsym value: 0.09 / % possible all: 98
Reflection
*PLUS
Num. obs: 22959 / Num. measured all: 239988 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 98 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 3.2

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Processing

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

1fe7
PDB Unreleased entry


Resolution: 1.8→11.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2042260.78 / 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
Rfree0.225 1100 4.8 %RANDOM
Rwork0.205 ---
all0.21 22959 --
obs0.205 22747 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.0477 Å2 / ksol: 0.332842 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.75 Å20 Å2
3---0.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å-0.03 Å
Refinement stepCycle: LAST / Resolution: 1.8→11.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 16 279 2230
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.027
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it3.322
X-RAY DIFFRACTIONc_scangle_it4.572.5
LS refinement shellResolution: 1.8→1.84 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.207 185 4.8 %
Rwork0.196 3708 -
obs-1581 96.2 %
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 DIFFRACTION4PAR.PARAMTOP.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.4

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