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- PDB-1psj: ACIDIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS -

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Basic information

Entry
Database: PDB / ID: 1psj
TitleACIDIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / LIPID DEGRADATION / CALCIUM
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / 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, 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 speciesGloydius halys (Halys viper)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2 Å
AuthorsWang, X.Q. / Lin, Z.J.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of an acidic phospholipase A2 from the venom of Agkistrodon halys pallas at 2.0 A resolution.
Authors: Wang, X.Q. / Yang, J. / Gui, L.L. / Lin, Z.J. / Chen, Y.C. / Zhou, Y.C.
#1: Journal: Chin.Sci.Bull. / Year: 1992
Title: Preliminary Crystallographic Study of the Platelet Aggregation Inhibitor from the Venom of Agkistrodon Halys Pallas
Authors: Gui, L. / Niu, X. / Bi, R. / Lin, Z. / Chen, Y.
History
DepositionMay 24, 1995Processing site: BNL
Revision 1.0Jul 11, 1996Provider: 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 ...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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0292
Polymers13,9891
Non-polymers401
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.570, 83.570, 32.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13988.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gloydius halys (Halys viper) / Secretion: VENOM / References: UniProt: P14418, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AMINO ACID NUMBERING IS BASED ON THE COMMON SCHEME PROPOSED FOR ALL PHOSPHOLIPASES. IT IS NOT CONSECUTIVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.94 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.05 M1dropNa(CH3)2AsO2-HCl
310 %(v/v)2,5-hexanediol1drop
465 %2,5-hexanediol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→29.81 Å / Num. obs: 7841 / % possible obs: 86.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.042
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 7861 / % possible obs: 87 % / Rmerge(I) obs: 0.0418

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3model building
X-PLOR3refinement
XENGENdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: molecular replacement / Resolution: 2→6 Å / σ(F): 2.01
Details: THE SIDE CHAINS OF RESIDUES LYS 124, GLN 128 AND GLU 129 AT C-TERMINAL LOOP HAVE LESS WELL DEFINED ELECTRON DENSITY. IT MAY BE A REFLECTION OF THE INTRINSIC FLEXIBILITY OF THIS PART OF THE MOLECULE.
RfactorNum. reflection% reflection
Rfree0.228 --
Rwork0.157 --
obs0.157 7481 87.6 %
Displacement parametersBiso mean: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 0 133 1103
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.644
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.85
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.205
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.69
X-RAY DIFFRACTIONx_dihedral_angle_d22.857

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