2V02 | pdb_00002v02

Recombinant vertebrate calmodulin complexed with Ba

• PDB DOI: https://doi.org/10.2210/pdb2V02/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-05-04 Released: 2007-08-14 
• Deposition Author(s): Kursula, P., Majava, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.294 (Depositor) 
• R-Value Work: 
  0.243 (Depositor) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

A Structural Insight Into Lead Neurotoxicity and Calmodulin Activation by Heavy Metals.

Kursula, P., Majava, V.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 653

• PubMed: 17671360 
• DOI: https://doi.org/10.1107/S1744309107034525
• Primary Citation Related Structures: 
  2V01, 2V02


• PubMed Abstract: 
  

  Calmodulin is a calcium sensor that is also capable of binding and being activated by other metal ions. Of specific interest in this respect is lead, which is known to be neurotoxic and to have a very high affinity towards calmodulin. Crystal structures of human calmodulin complexed with lead and barium ions have been solved. The results will help in understanding the activation mechanisms of calmodulin by different heavy metals and will provide a detailed view of a putative target for lead neurotoxicity in humans.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oulu, Oulu, Finland. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 17.25 kDa 
• Atom Count: 1,135 
• Modeled Residue Count: 142 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CALMODULIN	A	149	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23  Go to UniProtKB:  P0DP23
PHAROS:  P0DP23 GTEx:  ENSG00000198668

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BA	C [auth A], F [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
CA	B [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.294 (Depositor) 
• R-Value Work:  0.243 (Depositor) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.41	α = 89.84
b = 29.32	β = 85.68
c = 53.32	γ = 82.8

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Kursula, P., Majava, V.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 1.4: 2018-03-07
  Changes: Source and taxonomy
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description