1ZL7 | pdb_00001zl7

Crystal structure of catalytically-active phospholipase A2 with bound calcium

• PDB DOI: https://doi.org/10.2210/pdb1ZL7/pdb

• Classification: HYDROLASE
• Organism(s): Bothrops jararacussu
• Mutation(s): No 


• Deposited: 2005-05-05 Released: 2006-04-25 
• Deposition Author(s): Murakami, M.T., Cintra, A.C., Gabdoulkhakov, A., Genov, N., Betzel, C., Arni, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.232 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Insights into metal ion binding in phospholipases A(2): ultra high-resolution crystal structures of an acidic phospholipase A(2) in the Ca(2+) free and bound states.

Murakami, M.T., Gabdoulkhakov, A., Genov, N., Cintra, A.C., Betzel, C., Arni, R.K.

(2006) Biochimie 88: 543-549

• PubMed: 16376474 
• DOI: https://doi.org/10.1016/j.biochi.2005.10.014
• Primary Citation Related Structures: 
  1ZL7, 1ZLB


• PubMed Abstract: 
  

  The electrophile Ca(2+) is an essential multifunctional co-factor in the phospholipase A(2) mediated hydrolysis of phospholipids. Crystal structures of an acidic phospholipase A(2) from the venom of Bothrops jararacussu have been determined both in the Ca(2+) free and bound states at 0.97 and 1.60 A resolutions, respectively. In the Ca(2+) bound state, the Ca(2+) ion is penta-coordinated by a distorted pyramidal cage of oxygen and nitrogen atoms that is significantly different to that observed in structures of other Group I/II phospholipases A(2). In the absence of Ca(2+), a water molecule occupies the position of the Ca(2+) ion and the side chain of Asp49 and the calcium-binding loop adopts a different conformation.

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Organizational Affiliation: 
• Department of Physics, IBILCE/UNESP, Cristovão Colombo 2265, São José do Rio Preto, SP 15054-000, Brazil.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 13.83 kDa 
• Atom Count: 1,080 
• Modeled Residue Count: 122 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypotensive phospholipase A2	A	122	Bothrops jararacussu	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for Q8AXY1 (Bothrops jararacussu) Explore Q8AXY1  Go to UniProtKB:  Q8AXY1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.232 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.206	α = 90
b = 53.218	β = 90
c = 90.057	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-25 
Deposition Author(s): Murakami, M.T., Cintra, A.C., Gabdoulkhakov, A., Genov, N., Betzel, C., Arni, R.K.

Revision History  

• Version 1.0: 2006-04-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary