1B1G

SOLVATED REFINEMENT OF CA-LOADED CALBINDIN D9K


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: ALL CONFORMERS USED 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2BCB - determined by Kordel, J., Skelton, N.J., Akke, M., Chazin, W.J.  

Literature

Protein solution structure calculations in solution: solvated molecular dynamics refinement of calbindin D9k.

Kordel, J.Pearlman, D.A.Chazin, W.J.

(1997) J.Biomol.NMR 10: 231-243


  • PubMed Abstract: 
  • The three-dimensional solution structures of proteins determined with NMR-derived constraints are almost always calculated in vacuo. The solution structure of (Ca2+)2-calbindin D9k has been redetermined by new restrained molecular dynamics (MD) calcu ...

    The three-dimensional solution structures of proteins determined with NMR-derived constraints are almost always calculated in vacuo. The solution structure of (Ca2+)2-calbindin D9k has been redetermined by new restrained molecular dynamics (MD) calculations that include Ca2+ ions and explicit solvent molecules. Four parallel sets of MD refinements were run to provide accurate comparisons of structures produced in vacuo, in vacuo with Ca2+ ions, and with two different protocols in a solvent bath with Ca2+ ions. The structural ensembles were analyzed in terms of structural definition, molecular energies, packing density, solvent-accessible surface, hydrogen bonds, and the coordination of calcium ions in the two binding loops. Refinement including Ca2+ ions and explicit solvent results in significant improvements in the precision and accuracy of the structure, particularly in the binding loops. These results are consistent with results previously obtained in free MD simulations of proteins in solution and show that the rMD refined NMR-derived solution structures of proteins, especially metalloproteins, can be significantly improved by these strategies.


    Related Citations: 
    • High-Resolution Solution Structure of Calcium-Loaded Calbindin D9k
      Kordel, J.,Skelton, N.J.,Akke, M.,Chazin, W.J.
      (1993) J.Mol.Biol. 231: 711
    • 1H NMR Sequential Resonance Assignments, Secondary Structure, and Global Fold in Solution of the Major (Trans-Pro43) Form of Bovine Calbindin D9k
      Kordel, J.,Forsen, S.,Chazin, W.J.
      (1989) Biochemistry 28: 7065
    • The Rate and Structural Consequences of Proline Cis-Trans Isomerization in Calbindin D9k: NMR Studies of the Minor (Cis-Pro43) Isoform and the Pro43Gly Mutant
      Kordel, J.,Forsen, S.,Drakenberg, T.,Chazin, W.J.
      (1990) Biochemistry 29: 4400
    • The Refined Structure of Vitamin D-Dependent Calcium-Binding Protein from Bovine Intestine. Molecular Details, Ion Binding, and Implications for the Structure of Other Calcium-Binding Proteins
      Szebenyi, D.M.E.,Moffat, K.
      (1986) J.Biol.Chem. 261: 8761


    Organizational Affiliation

    Pharmacia & Upjohn, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CALBINDIN D9K)
A
75Bos taurusGene Names: S100G (CALB3, S100D)
Find proteins for P02633 (Bos taurus)
Go to Gene View: S100G
Go to UniProtKB:  P02633
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: ALL CONFORMERS USED 
  • Olderado: 1B1G Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-25
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-08-10
    Type: Other