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- PDB-1vip: ANTICOAGULANT CLASS II PHOSPHOLIPASE A2 FROM THE VENOM OF VIPERA ... -

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Basic information

Entry
Database: PDB / ID: 1vip
TitleANTICOAGULANT CLASS II PHOSPHOLIPASE A2 FROM THE VENOM OF VIPERA RUSSELLI RUSSELLI
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / PHOSPHOLIPASE A2 / ANTICOAGULANT
Function / homology
Function and homology information


phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / phospholipase A2 / 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 / 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
Basic phospholipase A2 RVV-VD
Similarity search - Component
Biological speciesDaboia russellii russellii (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCarredano, E. / Westerlund, B. / Persson, B. / Saarinen, M. / Ramaswamy, S. / Eaker, D. / Eklund, H.
CitationJournal: Toxicon / Year: 1998
Title: The three-dimensional structures of two toxins from snake venom throw light on the anticoagulant and neurotoxic sites of phospholipase A2.
Authors: Carredano, E. / Westerlund, B. / Persson, B. / Saarinen, M. / Ramaswamy, S. / Eaker, D. / Eklund, H.
History
DepositionFeb 27, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: 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

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7412
Polymers13,6441
Non-polymers961
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PHOSPHOLIPASE A2
hetero molecules

A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4814
Polymers27,2892
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation28_566x,-y+1,-z+3/21
Buried area3020 Å2
ΔGint-40 kcal/mol
Surface area11470 Å2
MethodPISA, PQS
3
A: PHOSPHOLIPASE A2
hetero molecules

A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4814
Polymers27,2892
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_564z+1/4,-y+5/4,x-1/41
Buried area590 Å2
ΔGint-33 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.782, 122.782, 122.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-300-

SO4

21A-292-

HOH

31A-293-

HOH

41A-294-

HOH

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13644.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MIAMI SERPENTARIUM / Source: (natural) Daboia russellii russellii (snake) / Secretion: VENOM / Species: Daboia russellii / Strain: russellii / References: UniProt: P81458, phospholipase A2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.81 Å3/Da / Density % sol: 51 %
Crystal growpH: 6.25
Details: PROTEIN WAS CRYSTALLIZED FROM 1.4 M AMSO4,N50 MM AMOAC AND 2 % DIOXANE AT PH 6.25.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 Mammonium sulfate1reservoir
250 mM1reservoirNH4Ac
32 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 8, 1993 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 8258 / % possible obs: 99.2 % / Observed criterion σ(I): 0.001 / Redundancy: 7.2 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.079 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.039 / % possible all: 98.5
Reflection
*PLUS
Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.855

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PP2

1pp2


Resolution: 2.2→25 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 658 8 %RANDOM
Rwork0.208 ---
obs0.208 8258 99.2 %-
Displacement parametersBiso mean: 34.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 5 94 1045
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.57
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.83
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
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.331 60 5.9 %
Rwork0.304 930 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19X.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.83

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