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- PDB-1fv0: FIRST STRUCTURAL EVIDENCE OF THE INHIBITION OF PHOSPHOLIPASE A2 B... -

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Basic information

Entry
Database: PDB / ID: 1fv0
TitleFIRST STRUCTURAL EVIDENCE OF THE INHIBITION OF PHOSPHOLIPASE A2 BY ARISTOLOCHIC ACID: CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND ARISTOLOCHIC ACID
ComponentsPHOSPHOLIPASE A2
KeywordsTOXIN / phospholipase A2 / Daboia russelli pulchella / neurotoxic / edema
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
9-HYDROXY ARISTOLOCHIC ACID / ACETATE ION / 1,4-DIETHYLENE DIOXIDE / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChandra, V. / Jasti, J. / Kaur, P. / Srinivasan, A. / Betzel, C. / Singh, T.P.
Citation
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.
#1: Journal: To be Published
Title: First structural evidence of antiinflammatory action of vitamin E (2,5,7,8-tetramethyl-2-(4',8',12'-trimethyltridecyl)-6-chromanol) through its binding to phospholipase A2 specifically: ...Title: First structural evidence of antiinflammatory action of vitamin E (2,5,7,8-tetramethyl-2-(4',8',12'-trimethyltridecyl)-6-chromanol) through its binding to phospholipase A2 specifically: Crystal structure of a complex formed between phospholipase A2 and vitamin E at 1.80 resolution
Authors: Chandra, V. / Jasti, J. / Kaur, P. / Perbandt, M. / Betzel, C.H. / Singh, T.P.
#2: 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.
History
DepositionSep 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Aug 9, 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 1.7Nov 20, 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
B: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,42012
Polymers27,2602
Non-polymers1,16110
Water5,675315
1
A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3306
Polymers13,6301
Non-polymers7015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0906
Polymers13,6301
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: PHOSPHOLIPASE A2
hetero molecules

A: PHOSPHOLIPASE A2
hetero molecules

B: PHOSPHOLIPASE A2
hetero molecules

B: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,84124
Polymers54,5194
Non-polymers2,32220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
Buried area8530 Å2
ΔGint-118 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.050, 89.480, 76.870
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-852-

HOH

21B-788-

HOH

31B-798-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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) / Secretion: VENOM / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071

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Non-polymers , 6 types, 325 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-9AR / 9-HYDROXY ARISTOLOCHIC ACID / 9-HYDROXY-8-METHOXY-6-NITRO-PHENANTHROL[3,4-D][1,3]DIOXOLE-5-CARBOXYLIC ACID


Mass: 357.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11NO8
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 50.97 %
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
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMsodium cacodylate1droppH7.0
215 mg/mlprotein1drop
31.2 Mammonium sulfate1reservoir
41 mM1reservoirCaCl2
53 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98
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: 1.7→30 Å / Num. all: 29231 / Num. obs: 29231 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 10.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.182 / % possible all: 97.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 28922 / % possible obs: 99.1 % / Num. measured all: 419758
Reflection shell
*PLUS
% possible obs: 97.9 % / Rmerge(I) obs: 0.034

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CL5

1cl5


Resolution: 1.7→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1442367.33 / 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
Rfree0.201 1413 4.9 %RANDOM
Rwork0.184 ---
all0.212 28818 --
obs0.212 28818 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.8357 Å2 / ksol: 0.424778 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2--0.56 Å20 Å2
3---0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 74 315 2277
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.651.5
X-RAY DIFFRACTIONc_mcangle_it1.152
X-RAY DIFFRACTIONc_scbond_it1.122
X-RAY DIFFRACTIONc_scangle_it1.642.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 260 5.5 %
Rwork0.243 4443 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ARN.PARAMARN.TOP
X-RAY DIFFRACTION5PAR.PARAMTOP.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.82

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