Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.38 kDa 
• Atom Count: 1297 
• Residue Count: 148 
• Unique protein chains: 1

1RFJ

Crystal Structure of Potato Calmodulin PCM6

• DOI: 10.2210/pdb1RFJ/pdb

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


• Deposited: 2003-11-10 Released: 2004-06-29 
• Deposition Author(s): Liang, D.C., Yun, C.H., Chang, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Literature

Structure of potato calmodulin PCM6: the first report of the three-dimensional structure of a plant calmodulin.

Yun, C.H., Bai, J., Sun, D.Y., Cui, D.F., Chang, W.R., Liang, D.C.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1214-1219

• PubMed: 15213382 
• DOI: 10.1107/S0907444904009771
• Primary Citation of Related Structures:  
  1RFJ


• PubMed Abstract: 
  

The crystal structure of a potato calmodulin (PCM6) was solved by molecular replacement and refined to a crystallographic R factor of 22.8% (R(free) = 25.0%) using X-ray diffraction data in the resolution range 8.0-2.0 A. This is the first report of the three-dimensional structure of a plant Ca(2+)-calmodulin. PCM6 crystallizes in a crystal form that belongs to space group P2(1)2(1)2(1), which is different to that of most other calmodulin crystals. The main structural difference between PCM6 and the other calmodulins is in the central helix region and appears to be caused by crystal packing. The surface properties of PCM6 molecules were compared with those of animal calmodulins, which provided an explanation for the unique crystal-packing state of PCM6.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
calmodulin	A	149	Solanum tuberosum	Mutation(s): 0  Gene Names: PCM6, PCM5, PCM7, PCM8
Find proteins for Q7DMN9 (Solanum tuberosum) Explore Q7DMN9  Go to UniProtKB:  Q7DMN9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.44	α = 90
b = 68.98	β = 90
c = 109.89	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-10 
• Released Date: 2004-06-29 
Deposition Author(s): Liang, D.C., Yun, C.H., Chang, W.R.

Revision History 

• Version 1.0: 2004-06-29
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description