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PDBsum entry 2pvb

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protein ligands metals links
Metal binding protein PDB id
2pvb
Jmol
Contents
Protein chain
108 a.a. *
Ligands
NH4
FMT ×2
Metals
_CA ×2
Waters ×211
* Residue conservation analysis
PDB id:
2pvb
Name: Metal binding protein
Title: Pike parvalbumin (pi 4.10) at low temperature (100k) and atomic resolution (0.91 a).
Structure: Protein (parvalbumin). Chain: a. Other_details: (pike pi 4.10)
Source: Esox lucius. Northern pike. Organism_taxid: 8010. Tissue: muscle
Resolution:
0.91Å     R-factor:   0.110     R-free:   0.132
Authors: J.P.Declercq,C.Evrard
Key ref: J.P.Declercq et al. (1999). Crystal structure of the EF-hand parvalbumin at atomic resolution (0.91 A) and at low temperature (100 K). Evidence for conformational multistates within the hydrophobic core. Protein Sci, 8, 2194-2204. PubMed id: 10548066 DOI: 10.1110/ps.8.10.2194
Date:
02-Oct-98     Release date:   07-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02619  (PRVB_ESOLU) -  Parvalbumin beta
Seq:
Struc:
107 a.a.
107 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     2 terms  

 

 
DOI no: 10.1110/ps.8.10.2194 Protein Sci 8:2194-2204 (1999)
PubMed id: 10548066  
 
 
Crystal structure of the EF-hand parvalbumin at atomic resolution (0.91 A) and at low temperature (100 K). Evidence for conformational multistates within the hydrophobic core.
J.P.Declercq, C.Evrard, V.Lamzin, J.Parello.
 
  ABSTRACT  
 
Several crystal structures of parvalbumin (Parv), a typical EF-hand protein, have been reported so far for different species with the best resolution achieving 1.5 A. Using a crystal grown under microgravity conditions, cryotechniques (100 K), and synchrotron radiation, it has now been possible to determine the crystal structure of the fully Ca2+-loaded form of pike (component pI 4.10) Parv.Ca2 at atomic resolution (0.91 A). The availability of such a high quality structure offers the opportunity to contribute to the definition of the validation tools useful for the refinement of protein crystal structures determined to lower resolution. Besides a better definition of most of the elements in the protein three-dimensional structure than in previous studies, the high accuracy thus achieved allows the detection of well-defined alternate conformations, which are observed for 16 residues out of 107 in total. Among them, six occupy an internal position within the hydrophobic core and converge toward two small buried cavities with a total volume of about 60 A3. There is no indication of any water molecule present in these cavities. It is probable that at temperatures of physiological conditions there is a dynamic interconversion between these alternate conformations in an energy-barrier dependent manner. Such motions for which the amplitudes are provided by the present study will be associated with a time-dependent remodeling of the void internal space as part of a slow dynamics regime (millisecond timescales) of the parvalbumin molecule. The relevance of such internal dynamics to function is discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287610 M.T.Henzl, J.J.Tanner, and A.Tan (2011).
Solution structures of chicken parvalbumin 3 in the Ca(2+)-free and Ca(2+)-bound states.
  Proteins, 79, 752-764.
PDB codes: 2kyc 2kyf
20156445 J.P.Schuermann, A.Tan, J.J.Tanner, and M.T.Henzl (2010).
Structure of avian thymic hormone, a high-affinity avian beta-parvalbumin, in the Ca2+-free and Ca2+-bound states.
  J Mol Biol, 397, 991.
PDB codes: 2kqy 3fs7
19221587 K.Chen, and L.Kurgan (2009).
Investigation of atomic level patterns in protein--small ligand interactions.
  PLoS ONE, 4, e4473.  
19804740 O.B.Okan, A.R.Atilgan, and C.Atilgan (2009).
Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics.
  Biophys J, 97, 2080-2088.  
18645235 C.Dumas, and A.van der Lee (2008).
Macromolecular structure solution by charge flipping.
  Acta Crystallogr D Biol Crystallogr, 64, 864-873.  
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
15930636 R.A.Judge, E.H.Snell, M.J.van der Woerd, and E.H.Snell (2005).
Extracting trends from two decades of microgravity macromolecular crystallization history.
  Acta Crystallogr D Biol Crystallogr, 61, 763-771.  
15169955 C.A.Bottoms, J.P.Schuermann, S.Agah, M.T.Henzl, and J.J.Tanner (2004).
Crystal structure of rat alpha-parvalbumin at 1.05 Angstrom resolution.
  Protein Sci, 13, 1724-1734.
PDB code: 1rwy
15388862 M.Khalili, J.A.Saunders, A.Liwo, S.OƂdziej, and H.A.Scheraga (2004).
A united residue force-field for calcium-protein interactions.
  Protein Sci, 13, 2725-2735.  
12524313 E.Feinstein, G.Deikus, E.Rusinova, E.L.Rachofsky, J.B.Ross, and W.R.Laws (2003).
Constrained analysis of fluorescence anisotropy decay:application to experimental protein dynamics.
  Biophys J, 84, 599-611.  
11867433 M.S.Cates, M.L.Teodoro, and G.N.Phillips (2002).
Molecular mechanisms of calcium and magnesium binding to parvalbumin.
  Biophys J, 82, 1133-1146.  
12377126 R.Fourme, I.Ascone, R.Kahn, M.Mezouar, P.Bouvier, E.Girard, T.Lin, and J.E.Johnson (2002).
Opening the high-pressure domain beyond 2 kbar to protein and virus crystallography--technical advance.
  Structure, 10, 1409-1414.  
11114499 A.Lewit-Bentley, and S.Réty (2000).
EF-hand calcium-binding proteins.
  Curr Opin Struct Biol, 10, 637-643.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.