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- PDB-1pp2: THE REFINED CRYSTAL STRUCTURE OF DIMERIC PHOSPHOLIPASE A2 AT 2.5 ... -

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Basic information

Entry
Database: PDB / ID: 1pp2
TitleTHE REFINED CRYSTAL STRUCTURE OF DIMERIC PHOSPHOLIPASE A2 AT 2.5 ANGSTROMS. ACCESS TO A SHIELDED CATALYTIC CENTER
ComponentsCALCIUM-FREE PHOSPHOLIPASE A2
KeywordsHYDROLASE
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
Acidic phospholipase A2
Similarity search - Component
Biological speciesCrotalus atrox (western diamondback rattlesnake)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBrunie, S. / Sigler, P.B.
Citation
Journal: J.Biol.Chem. / Year: 1985
Title: The refined crystal structure of dimeric phospholipase A2 at 2.5 A. Access to a shielded catalytic center.
Authors: Brunie, S. / Bolin, J. / Gewirth, D. / Sigler, P.B.
#1: Journal: J.Biol.Chem. / Year: 1985
Title: A Comparison of the Crystal Structures of Phospholipase A2 from Bovine Pancreas and Crotalus Atrox Venom
Authors: Renetseder, R. / Brunie, S. / Dijkstra, B.W. / Drenth, J. / Sigler, P.B.
#2: Journal: J.Biol.Chem. / Year: 1981
Title: The 2.5 Angstroms Crystal Structure of a Dimeric Phospholipase A2 from the Venom of Crotalus Atrox
Authors: Keith, C. / Feldman, D.S. / Deganello, S. / Glick, J. / Ward, K.B. / Jones, E.O. / Sigler, P.B.
#3: Journal: J.Mol.Biol. / Year: 1975
Title: Characterization of Crystals of Two Venom Phospholipases A2
Authors: Pasek, M. / Keith, C. / Feldman, D. / Sigler, P.B.
History
DepositionMar 10, 1986Processing site: BNL
Revision 1.0May 7, 1986Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: CALCIUM-FREE PHOSPHOLIPASE A2
L: CALCIUM-FREE PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)27,2152
Polymers27,2152
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-18 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.400, 100.200, 48.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.12725, 0.1029, -0.98652), (0.09793, -0.98844, -0.11573), (-0.98702, -0.11134, 0.1157)
Vector: 61.65457, 79.66322, 62.94765)
DetailsTHE ENZYME IS A DIMER COMPOSED OF TWO IDENTICAL SUBUNITS OF 122 RESIDUES EACH. THE *RIGHT* SUBUNIT HAS BEEN ASSIGNED CHAIN IDENTIFIER *R*. THE *LEFT* SUBUNIT HAS BEEN ASSIGNED CHAIN IDENTIFIER *L*. THE TRANSFORMATION PRESENTED ON THE *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE *RIGHT* SUBUNIT (CHAIN *R*) WHEN APPLIED TO THE *LEFT* SUBUNIT (CHAIN *L*).

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Components

#1: Protein CALCIUM-FREE PHOSPHOLIPASE A2


Mass: 13607.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crotalus atrox (western diamondback rattlesnake)
References: UniProt: P00624, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM11NaCl
210 mMTris-HCl11
40.1 mM11CaCl2
510 mM12Na2EDTA
60.1 mM12CaCl2
3phospholipase A2 solution11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.178 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 0 137 2029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.028
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg4
X-RAY DIFFRACTIONp_planar_d
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
Refinement
*PLUS
σ(I): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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