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PDBsum entry 4cpv

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protein metals links
Calcium binding PDB id
4cpv
Jmol
Contents
Protein chain
109 a.a. *
Metals
_CA ×2
Waters ×74
* Residue conservation analysis
PDB id:
4cpv
Name: Calcium binding
Title: Refined crystal structure of calcium-liganded carp parvalbumin 4.25 at 1.5-angstroms resolution
Structure: Calcium-binding parvalbumin. Chain: a. Engineered: yes
Source: Cyprinus carpio. Common carp. Organism_taxid: 7962
Resolution:
1.50Å     R-factor:   0.215    
Authors: V.D.Kumar,L.Lee,B.F.P.Edwards
Key ref:
V.D.Kumar et al. (1990). Refined crystal structure of calcium-liganded carp parvalbumin 4.25 at 1.5-A resolution. Biochemistry, 29, 1404-1412. PubMed id: 2334704 DOI: 10.1021/bi00458a010
Date:
18-Oct-89     Release date:   15-Oct-90    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02618  (PRVB_CYPCA) -  Parvalbumin beta
Seq:
Struc:
108 a.a.
108 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: 10.1021/bi00458a010 Biochemistry 29:1404-1412 (1990)
PubMed id: 2334704  
 
 
Refined crystal structure of calcium-liganded carp parvalbumin 4.25 at 1.5-A resolution.
V.D.Kumar, L.Lee, B.F.Edwards.
 
  ABSTRACT  
 
The crystal structure of carp parvalbumin (pI = 4.25) has been refined by restrained least-squares analysis employing X-ray diffractometer data to 1.5-A resolution. The final residual for 12,653 reflections between 10 and 1.5 A with I(hkl) greater than 2 sigma(I) is 0.215. A total of 74 solvent molecules were included in the least-squares analysis. The root mean square deviation from ideality of bond lengths is 0.024 A. The model has a root mean square difference of 0.59 A from the positions of the main-chain atoms in a previously reported structure [Moews, P. C., & Kretsinger, R. H. (1975) J. Mol. Biol. 91, 201-228], which was refined by difference Fourier syntheses using data collected by film to 1.9 A. Although the overall features of the two models are very similar, there are significant differences in the amino-terminal region, which was extensively refit, and in the number of oxygen atoms liganding calcium in the CD and EF sites, which increased from six to seven in the CD site and decreased from eight to seven in the EF site.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21262274 Z.Grabarek (2011).
Insights into modulation of calcium signaling by magnesium in calmodulin, troponin C and related EF-hand proteins.
  Biochim Biophys Acta, 1813, 913-921.  
19651438 S.E.Permyakov, A.G.Bakunts, M.E.Permyakova, A.I.Denesyuk, V.N.Uversky, and E.A.Permyakov (2009).
Metal-controlled interdomain cooperativity in parvalbumins.
  Cell Calcium, 46, 163-175.  
17567747 N.Juranić, E.Atanasova, J.H.Streiff, S.Macura, and F.G.Prendergast (2007).
Solvent-induced differentiation of protein backbone hydrogen bonds in calmodulin.
  Protein Sci, 16, 1329-1337.  
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
14573874 N.Juranić, S.Macura, and F.G.Prendergast (2003).
H-bonding mediates polarization of peptide groups in folded proteins.
  Protein Sci, 12, 2633-2636.  
  10739249 R.C.Richardson, N.M.King, D.J.Harrington, H.Sun, W.E.Royer, and D.J.Nelson (2000).
X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B).
  Protein Sci, 9, 73-82.
PDB code: 1bu3
10081963 J.A.Cuff, and G.J.Barton (1999).
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.
  Proteins, 34, 508-519.  
  10548066 J.P.Declercq, C.Evrard, V.Lamzin, and J.Parello (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.
PDB code: 2pvb
9585577 R.R.Biekofsky, S.R.Martin, J.P.Browne, P.M.Bayley, and J.Feeney (1998).
Ca2+ coordination to backbone carbonyl oxygen atoms in calmodulin and other EF-hand proteins: 15N chemical shifts as probes for monitoring individual-site Ca2+ coordination.
  Biochemistry, 37, 7617-7629.  
9235002 A.L.Lomize, and H.I.Mosberg (1997).
Thermodynamic model of secondary structure for alpha-helical peptides and proteins.
  Biopolymers, 42, 239-269.  
9154918 M.Laberge, W.W.Wright, K.Sudhakar, P.A.Liebman, and J.M.Vanderkooi (1997).
Conformational effects of calcium release from parvalbumin: comparison of computational simulations with spectroscopic investigations.
  Biochemistry, 36, 5363-5371.  
  9236210 S.K.Drake, M.A.Zimmer, C.Kundrot, and J.J.Falke (1997).
Molecular tuning of an EF-hand-like calcium binding loop. Contributions of the coordinating side chain at loop position 3.
  J Gen Physiol, 110, 173-184.  
  9385642 S.P.Revett, G.King, J.Shabanowitz, D.F.Hunt, K.L.Hartman, T.M.Laue, and D.J.Nelson (1997).
Characterization of a helix-loop-helix (EF hand) motif of silver hake parvalbumin isoform B.
  Protein Sci, 6, 2397-2408.
PDB code: 1bu3
  9164648 E.C.Tozer, P.E.Hughes, and J.C.Loftus (1996).
Ligand binding and affinity modulation of integrins.
  Biochem Cell Biol, 74, 785-798.  
8639655 S.K.Drake, and J.J.Falke (1996).
Kinetic tuning of the EF-hand calcium binding motif: the gateway residue independently adjusts (i) barrier height and (ii) equilibrium.
  Biochemistry, 35, 1753-1760.  
8639620 S.K.Drake, K.L.Lee, and J.J.Falke (1996).
Tuning the equilibrium ion affinity and selectivity of the EF-hand calcium binding motif: substitutions at the gateway position.
  Biochemistry, 35, 6697-6705.  
7896823 A.C.da Silva, J.Kendrick-Jones, and F.C.Reinach (1995).
Determinants of ion specificity on EF-hands sites. Conversion of the Ca2+/Mg2+ site of smooth muscle myosin regulatory light chain into a Ca(2+)-specific site.
  J Biol Chem, 270, 6773-6778.  
7607221 K.Sudhakar, M.Erecinska, and J.M.Vanderkooi (1995).
Interaction of polyamines with the Ca(2+)-binding protein parvalbumin.
  Eur J Biochem, 230, 498-502.  
7899550 J.J.Falke, S.K.Drake, A.L.Hazard, and O.B.Peersen (1994).
Molecular tuning of ion binding to calcium signaling proteins.
  Q Rev Biophys, 27, 219-290.  
  8003986 K.Y.Zhang, and D.Eisenberg (1994).
The three-dimensional profile method using residue preference as a continuous function of residue environment.
  Protein Sci, 3, 687-695.  
  7909511 P.Stanley, P.A.Bates, J.Harvey, R.I.Bennett, and N.Hogg (1994).
Integrin LFA-1 alpha subunit contains an ICAM-1 binding site in domains V and VI.
  EMBO J, 13, 1790-1798.  
8453652 C.Andressen, I.Blümcke, and M.R.Celio (1993).
Calcium-binding proteins: selective markers of nerve cells.
  Cell Tissue Res, 271, 181-208.  
8354278 U.G.Föhr, B.R.Weber, M.Müntener, W.Staudenmann, G.J.Hughes, S.Frutiger, D.Banville, B.W.Schäfer, and C.W.Heizmann (1993).
Human alpha and beta parvalbumins. Structure and tissue-specific expression.
  Eur J Biochem, 215, 719-727.  
1932565 M.T.Foffani, R.Battistutta, A.Calderan, P.Ruzza, G.Borin, and E.Peggion (1991).
Conformational and binding studies on peptides related to domains I and III of calmodulin.
  Biopolymers, 31, 671-681.  
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 code is shown on the right.