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- PDB-1vpi: PHOSPHOLIPASE A2 INHIBITOR FROM VIPOXIN -

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Basic information

Entry
Database: PDB / ID: 1vpi
TitlePHOSPHOLIPASE A2 INHIBITOR FROM VIPOXIN
ComponentsPHOSPHOLIPASE A2 INHIBITOR
KeywordsNEUROTOXIN / PHOSPHOLIPASE A2 INHIBITOR / RECOGNITION / MOLECULAR EVOLUTION
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / negative regulation of T cell proliferation / lipid catabolic process / 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 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Acidic phospholipase A2 homolog vipoxin A chain
Similarity search - Component
Biological speciesVipera ammodytes (sand viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDevedjiev, Y.D. / Popov, A.N.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: X-ray structure at 1.76 A resolution of a polypeptide phospholipase A2 inhibitor.
Authors: Devedjiev, Y. / Popov, A. / Atanasov, B. / Bartunik, H.D.
#1: Journal: Eur.Cryst.Meeting / Year: 1994
Title: Structure and Mechanism of Phospholipase A2
Authors: Devedjiev, Y. / Popov, A. / Bartunik, H.-D. / Atanasov, B.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystals of Phospholipase A2 Inhibitor. The Non-Toxic Component of Vipoxin from the Venom of Bulgarian Viper (Vipera Ammodytes)
Authors: Devedjiev, Y. / Atanasov, B. / Mancheva, I. / Aleksiev, B.
#3: Journal: Dokl.Bolg.Akad.Nauk / Year: 1989
Title: Solubility and Phase States of Vipoxin from the Venom of Bulgarian Viper (Vipera Ammodytes Ammodytes)
Authors: Devedjiev, Y.D. / Mancheva, I.N. / Aleksiev, B.V. / Atanasov, B.P.
History
DepositionDec 17, 1996Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 INHIBITOR


Theoretical massNumber of molelcules
Total (without water)13,6501
Polymers13,6501
Non-polymers00
Water2,090116
1
A: PHOSPHOLIPASE A2 INHIBITOR

A: PHOSPHOLIPASE A2 INHIBITOR


Theoretical massNumber of molelcules
Total (without water)27,3002
Polymers27,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2870 Å2
ΔGint-20 kcal/mol
Surface area10950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.900, 68.900, 52.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

21A-170-

HOH

31A-175-

HOH

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Components

#1: Protein PHOSPHOLIPASE A2 INHIBITOR


Mass: 13650.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vipera ammodytes (sand viper) / Organ: VENOM GLAND / References: UniProt: P04084
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 8.3
Details: PROTEIN WAS CRYSTALLIZED FROM 52% AMMONIUM SULFATE, 0.5% MPD, 100 MM TRIS, PH 8.3
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
252 %satammonium sulfate1reservoir
30.1 MTris-HCl1reservoir
40.5 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: OIIF, DUBNA, RUSSIA / Detector: AREA DETECTOR / Date: Jun 1, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.76 Å / Num. obs: 11854 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.058
Reflection shellResolution: 1.76→1.86 Å / % possible all: 48
Reflection
*PLUS
Num. measured all: 42158
Reflection shell
*PLUS
% possible obs: 48 %

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Processing

Software
NameVersionClassification
LOCALdata collection
BLANCdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
IN-HOUSESOFTWAREdata reduction
BLANCdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PP2

1pp2


Resolution: 1.76→6 Å / σ(F): 2.5
RfactorNum. reflection% reflection
Rwork0.155 --
obs0.155 9825 98 %
Displacement parametersBiso mean: 24.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 1.76→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 0 116 1063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55

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