1UHN | pdb_00001uhn

The crystal structure of the calcium binding protein AtCBL2 from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb1UHN/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-07-07 Released: 2003-11-04 
• Deposition Author(s): Nagae, M., Nozawa, A., Koizumi, N., Sano, H., Hashimoto, H., Sato, M., Shimizu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.248 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

The Crystal Structure of the Novel Calcium-binding Protein AtCBL2 from Arabidopsis thaliana

Nagae, M., Nozawa, A., Koizumi, N., Sano, H., Hashimoto, H., Sato, M., Shimizu, T.

(2003) J Biological Chem 278: 42240-42246

• PubMed: 12871972 
• DOI: https://doi.org/10.1074/jbc.M303630200
• Primary Citation Related Structures: 
  1UHN


• PubMed Abstract: 
  

  Arabidopsis thaliana calcineurin B-like protein (AtCBL2) is a member of a recently identified family of calcineurin B-like calcium-binding proteins in A. thaliana. The crystal structure of AtCBL2 has been determined at 2.1 A resolution. The protein forms a compact alpha-helical structure with two pairs of EF-hand motifs. The structure is similar in overall folding topology to the structures of calcineurin B and neuronal calcium sensor 1, but differs significantly in local conformation. The two calcium ions are coordinated in the first and fourth EF-hand motifs, whereas the second and third EF-hand motifs are maintained in the open form by internal hydrogen bonding without coordination of calcium ions. Both a possible site and a possible mechanism for the target binding to AtCBL2 are discussed based on the three-dimensional structure.

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Organizational Affiliation: 
• Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.99 kDa 
• Atom Count: 1,684 
• Modeled Residue Count: 189 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
calcineurin B-like protein 2	A	189	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q8LAS7 (Arabidopsis thaliana) Explore Q8LAS7  Go to UniProtKB:  Q8LAS7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.248 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.9	α = 90
b = 118.1	β = 90
c = 49.1	γ = 90

Software Package:

Software Name	Purpose
Crystal	data collection
Crystal	data reduction
SOLVE	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-04 
Deposition Author(s): Nagae, M., Nozawa, A., Koizumi, N., Sano, H., Hashimoto, H., Sato, M., Shimizu, T.

Revision History  

• Version 1.0: 2003-11-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations