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- PDB-1ppa: THE CRYSTAL STRUCTURE OF A LYSINE 49 PHOSPHOLIPASE A2 FROM THE VE... -

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Basic information

Entry
Database: PDB / ID: 1ppa
TitleTHE CRYSTAL STRUCTURE OF A LYSINE 49 PHOSPHOLIPASE A2 FROM THE VENOM OF THE COTTONMOUTH SNAKE AT 2.0 ANGSTROMS RESOLUTION
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE(CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


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
ANILINE / Basic phospholipase A2 homolog AppP2
Similarity search - Component
Biological speciesAgkistrodon piscivorus piscivorus (Eastern cottonmouth)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHolland, D.R. / Clancy, L.L. / Muchmore, S.W. / Rydel, T.J. / Einspahr, H.M. / Finzel, B.C. / Heinrikson, R.L. / Watenpaugh, K.D.
CitationJournal: J.Biol.Chem. / Year: 1990
Title: The crystal structure of a lysine 49 phospholipase A2 from the venom of the cottonmouth snake at 2.0-A resolution.
Authors: Holland, D.R. / Clancy, L.L. / Muchmore, S.W. / Ryde, T.J. / Einspahr, H.M. / Finzel, B.C. / Heinrikson, R.L. / Watenpaugh, K.D.
History
DepositionOct 29, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,0802
Polymers13,9871
Non-polymers931
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.530, 71.530, 57.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: THE SIDE GROUP OF SER 74 IS DISORDERED SUCH THAT TWO DISCRETE 'OG' POSITIONS APPEAR IN THE ELECTRON DENSITY MAP.

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13987.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agkistrodon piscivorus piscivorus (Eastern cottonmouth)
Species: Agkistrodon piscivorus / Strain: piscivorus / References: UniProt: P04361, phospholipase A2
#2: Chemical ChemComp-ANL / ANILINE


Mass: 93.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE SUBSTRATE CYLCLOHEXYLAMINE IS UNCERTAIN. IT WAS DESCRIBED AS A 'STRANGE DENSITY', MAYBE ...THE SUBSTRATE CYLCLOHEXYLAMINE IS UNCERTAIN. IT WAS DESCRIBED AS A 'STRANGE DENSITY', MAYBE DIOXANE, IN THE PRIMARY PUBLICATION. IT IS MORE LIKELY CYCLOHEXYLAMINE SINCE THE VENTILATING SYSTEM WAS SPREADING IT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
22.0-2.3 Mammonium sulfate1reservoir
350 mMCHES1reservoir
42 %(v/v)dioxane1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 10136 / Rmerge(I) obs: 0.08

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Processing

SoftwareName: CEDAR / Classification: refinement
RefinementResolution: 2→10 Å /
RfactorNum. reflection
Rwork0.157 -
obs-10003
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 7 151 1127
Software
*PLUS
Name: CEDAR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 10003 / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS

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