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- PDB-1aok: VIPOXIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1aok
TitleVIPOXIN COMPLEX
Components(VIPOXIN COMPLEX) x 2
KeywordsHYDROLASE / PHOSPHOLIPASE / VIPOXIN / PLA2-ACTIVITY / SNAKE-VENOM
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / killing of cells of another organism / 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
ACETATE ION / Acidic phospholipase A2 homolog vipoxin A chain / Basic phospholipase A2 vipoxin B chain
Similarity search - Component
Biological speciesVipera ammodytes meridionalis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPerbandt, M. / Wilson, J.C. / Eschenburg, S. / Betzel, C.
CitationJournal: FEBS Lett. / Year: 1997
Title: Crystal structure of vipoxin at 2.0 A: an example of regulation of a toxic function generated by molecular evolution.
Authors: Perbandt, M. / Wilson, J.C. / Eschenburg, S. / Mancheva, I. / Aleksiev, B. / Genov, N. / Willingmann, P. / Weber, W. / Singh, T.P. / Betzel, C.
History
DepositionJul 7, 1997Processing site: BNL
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: VIPOXIN COMPLEX
B: VIPOXIN COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5563
Polymers27,4972
Non-polymers591
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-20 kcal/mol
Surface area11210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.640, 67.690, 46.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein VIPOXIN COMPLEX / PHOSPHOLIPASE A2 INHIBITOR AND PHOSPHOLIPASE A2


Mass: 13661.036 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vipera ammodytes meridionalis (snake) / Secretion: VENOM / Species: Vipera ammodytes / Strain: meridionalis / References: UniProt: P04084, phospholipase A2
#2: Protein VIPOXIN COMPLEX / PHOSPHOLIPASE A2 INHIBITOR AND PHOSPHOLIPASE A2


Mass: 13835.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vipera ammodytes meridionalis (snake) / Secretion: VENOM / Species: Vipera ammodytes / Strain: meridionalis / References: UniProt: P14420, phospholipase A2
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN VIPOXIN ONE SUBUNIT IS ROTATED BY ABOUT 180 DEGREE TO GIVE A PSEUDO MIRROR SYMMETRY AND THE ...IN VIPOXIN ONE SUBUNIT IS ROTATED BY ABOUT 180 DEGREE TO GIVE A PSEUDO MIRROR SYMMETRY AND THE COMPLEX IS STABILIZED BY TWELVE INTERMOLECULAR CONTACTS WHICH OBVIOUSLY DIFFER FROM OTHER DIMERIC PHOSPHOLIPASES A2.

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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 Å3/Da / Density % sol: 36.88 %
Crystal growpH: 4.8 / Details: pH 4.8
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
214 %PEG33501reservoir
315 %PEG4001reservoir
410 mM1reservoirCaCl2
5100 mMNa acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1995 / Details: COLLIMATOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 15070 / % possible obs: 100 % / Observed criterion σ(I): 2 / Rsym value: 0.086
Reflection shellResolution: 2→2.03 Å / Rsym value: 0.274 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.274

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PP2

1pp2


Resolution: 2→20 Å /
Rfactor% reflection
Rfree0.23 5 %
Rwork0.16 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 4 291 2204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.034
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.025
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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