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- PDB-1kpm: First Structural Evidence of a Specific Inhibition of Phospholipa... -

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Basic information

Entry
Database: PDB / ID: 1kpm
TitleFirst Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution.
ComponentsPhospholipase A2
KeywordsHYDROLASE / phospholipase A2 / Daboia russelli pulchella / neurotoxic / inflammation
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / VITAMIN E / 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. / Betzel, C. / Srinivasan, A. / Singh, T.P.
Citation
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.
#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. / Betzel, C. / Srinivasan, A. / Singh, T.P.
#2: Journal: To be Published
Title: Crystal 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
Authors: Chandra, V. / Jasti, J. / Kaur, P. / Betzel, C. / Srinivasan, A. / Singh, T.P.
#3: Journal: To be Published
Title: First Structural Evidence of the Inhibition of Phospholipase A2 by Aristolochic Acid: Crystal Structure of a Complex Formed between Phospholipase A2 and Aristolochic Acid
Authors: Chandra, V. / Jasti, J. / Kaur, P. / Betzel, C. / Srinivasan, A. / Singh, T.P.
#4: Journal: To be Published
Title: Design 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
Authors: Chandra, V. / Jasti, J. / Kaur, P. / Betzel, C. / Srinivasan, A. / Singh, T.P.
#5: 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.
#6: Journal: J.Mol.Biol. / Year: 2000
Title: Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from Daboia russelli pulchella at 2.4 A resolution.
Authors: Chandra, V. / Kaur, P. / Srinivasan, A. / Singh, T.P.
History
DepositionJan 1, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionJul 10, 2002ID: 1FE7
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Aug 16, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,9307
Polymers27,2602
Non-polymers6715
Water5,513306
1
A: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1213
Polymers13,6301
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8104
Polymers13,6301
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.790, 88.510, 78.040
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-596-

HOH

21B-577-

HOH

31B-589-

HOH

41B-598-

HOH

51B-658-

HOH

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

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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) / Secretion: venom / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2
#2: Chemical ChemComp-VIT / VITAMIN E / 2,5,7,8-TETRAMETHYL-2-(4,8,12-TRIMETHYLTRIDECYL)-6-CHROMANOL / Vitamin E


Mass: 430.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50O2
#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.: 306 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
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 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
220 mMsodium cacodylate1droppH6.5
31.4 Mammonium sulfate1reservoir
43 %(v/v)dioxane1reservoir

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 1999 / Details: MIRRORS
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: 23652 / Num. obs: 23652 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.038 / Net I/σ(I): 9.93
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1609 / Rsym value: 0.084 / % possible all: 99
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % possible obs: 96 % / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 3

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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: 1.8→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high 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
Rfree0.228 1139 4.8 %RANDOM
Rwork0.197 ---
all0.197 23652 --
obs0.197 23652 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.6763 Å2 / ksol: 0.422816 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 31 322 2241
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
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_deg2.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.91.5
X-RAY DIFFRACTIONc_mcangle_it1.52
X-RAY DIFFRACTIONc_scbond_it1.362
X-RAY DIFFRACTIONc_scangle_it2.12.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 189 4.7 %
Rwork0.226 3803 -
obs-1609 98.8 %
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 DIFFRACTION4VIT.PARAMVIT.TOP
X-RAY DIFFRACTION5PAR.PARAMTOP.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg4.01

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