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- PDB-1clp: CRYSTAL STRUCTURE OF A CALCIUM-INDEPENDENT PHOSPHOLIPASELIKE MYOT... -

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Basic information

Entry
Database: PDB / ID: 1clp
TitleCRYSTAL STRUCTURE OF A CALCIUM-INDEPENDENT PHOSPHOLIPASELIKE MYOTOXIC PROTEIN FROM BOTHROPS ASPER VENOM
ComponentsMYOTOXIN II
KeywordsHYDROLASE
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / phospholipid metabolic process / negative regulation of T cell proliferation / phospholipid binding / heparin binding / toxin activity / defense response to bacterium / 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
Basic phospholipase A2 homolog 2
Similarity search - Component
Biological speciesBothrops asper (terciopelo)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsArni, R.K. / Ward, R.J. / Gutierrez, J.M. / Tulinsky, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of a calcium-independent phospholipase-like myotoxic protein from Bothrops asper venom.
Authors: Arni, R.K. / Ward, R.J. / Gutierrez, J.M. / Tulinsky, A.
#1: Journal: Toxicon / Year: 1993
Title: Crystallization and Preliminary Diffraction Data of Two Myotoxins Isolated from the Venoms of Bothrops Asper (Terciopelo) and Bothrops Nummifer (Jumping Viper)
Authors: Arni, R.K. / Gutierrez, J.M.
History
DepositionSep 12, 1994Processing site: BNL
Revision 1.0Nov 30, 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 / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOTOXIN II
B: MYOTOXIN II


Theoretical massNumber of molelcules
Total (without water)27,5282
Polymers27,5282
Non-polymers00
Water48627
1
A: MYOTOXIN II


Theoretical massNumber of molelcules
Total (without water)13,7641
Polymers13,7641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MYOTOXIN II


Theoretical massNumber of molelcules
Total (without water)13,7641
Polymers13,7641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.180, 67.760, 88.000
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: (0.3338, -0.0176, -0.9425), (0.01, -0.9997, 0.0222), (-0.9426, -0.0168, -0.3336)
Vector: -3.7156, 24.374, -5.8398)
DetailsMTRIX THE TRANSFORMATION PRESENTED ON MTRIX RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE *A* SUBUNIT WHEN APPLIED TO THE *B* SUBUNIT.

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Components

#1: Protein MYOTOXIN II


Mass: 13764.138 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bothrops asper (terciopelo) / References: UniProt: P24605, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
20.1 Macetate1reservoir
32.0 Mammonium sulfate1reservoir
41 mM1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 23021 / Observed criterion σ(I): 3
Reflection
*PLUS
Num. obs: 5805 / Num. measured all: 23021 / Rmerge(I) obs: 0.056

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→7 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.165 -
obs0.165 4915
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 0 27 1917
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.94
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d6.66
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.94
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg6.66

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