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- PDB-1a2a: AGKISTROTOXIN, A PHOSPHOLIPASE A2-TYPE PRESYNAPTIC NEUROTOXIN FRO... -

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Basic information

Entry
Database: PDB / ID: 1a2a
TitleAGKISTROTOXIN, A PHOSPHOLIPASE A2-TYPE PRESYNAPTIC NEUROTOXIN FROM AGKISTRODON HALYS PALLAS
ComponentsPHOSPHOLIPASE A2
KeywordsPRESYNAPTIC NEUROTOXIN / PHOSPHOLIPASE A2 / HYDROLASE / LIPID DEGRADATION
Function / homology
Function and homology information


phospholipase A2 / 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
Neutral phospholipase A2 agkistrodotoxin
Similarity search - Component
Biological speciesGloydius halys (Halys viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTang, L. / Zhou, Y. / Lin, Z.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of agkistrodotoxin, a phospholipase A2-type presynaptic neurotoxin from agkistrodon halys pallas.
Authors: Tang, L. / Zhou, Y.C. / Lin, Z.J.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Crystal Structure of Agkistrodotoxin, a Phospholipase A2-Type Presynaptic Neurotoxin from Agkistrodon Halys Pallas
Authors: Tang, L. / Zhou, Y.C. / Lin, Z.J.
History
DepositionDec 25, 1997Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
B: PHOSPHOLIPASE A2
C: PHOSPHOLIPASE A2
D: PHOSPHOLIPASE A2
E: PHOSPHOLIPASE A2
F: PHOSPHOLIPASE A2
G: PHOSPHOLIPASE A2
H: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,10612
Polymers110,9648
Non-polymers1424
Water00
1
A: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,8711
Polymers13,8711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,8711
Polymers13,8711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9062
Polymers13,8711
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9062
Polymers13,8711
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9062
Polymers13,8711
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9062
Polymers13,8711
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,8711
Polymers13,8711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)13,8711
Polymers13,8711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.950, 85.227, 71.054
Angle α, β, γ (deg.)90.00, 109.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PHOSPHOLIPASE A2 / AGKISTROTOXIN / ATX


Mass: 13870.562 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Gloydius halys (Halys viper) / References: UniProt: P14421, phospholipase A2
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 49 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
260 %MPD1drop
30.6 Mammonium sulfate1drop
41 %octyl-beta-D-glucopyranoside1drop
50.6 M1dropKCl
60.1 M1dropNaAc
760 %MPD1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1994 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.58→100 Å / Num. obs: 32147 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 9.42
Reflection shellResolution: 2.58→2.74 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.41 / % possible all: 26
Reflection
*PLUS
Highest resolution: 2.59 Å / % possible obs: 84.36 %

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
XENGENdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSJ

1psj


Resolution: 2.8→6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE ASYMMETRIC UNIT CONTAINS 8 MOLECULES. THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT METHOD USING A MONOMERIC SEARCH MODEL WHICH SHOWS 51 PERCENT SEQUENCE IDENTITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1419 10.2 %RANDOM
Rwork0.207 ---
obs0.207 13936 51.2 %-
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-5.5 Å
Luzzati sigma a0.52 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7688 0 4 0 7692
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.991.5
X-RAY DIFFRACTIONx_mcangle_it4.72
X-RAY DIFFRACTIONx_scbond_it5.082
X-RAY DIFFRACTIONx_scangle_it7.462.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.8→2.96 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 157 9.2 %
Rwork0.279 1558 -
obs--37.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.59
LS refinement shell
*PLUS
Rfactor obs: 0.279

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