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PDBsum entry 1a19
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protein Protein-protein interface(s) links
Ribonuclease inhibitor PDB id
1a19

 

 

 

 

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Contents
Protein chains
89 a.a. *
* Residue conservation analysis
PDB id:
1a19
Name: Ribonuclease inhibitor
Title: Barstar (free), c82a mutant
Structure: Barstar. Chain: a, b. Engineered: yes. Mutation: yes
Source: Bacillus amyloliquefaciens. Organism_taxid: 1390. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.76Å     R-factor:   0.203     R-free:   0.292
Authors: G.S.Ratnaparkhi,R.Varadarajan
Key ref:
G.S.Ratnaparkhi et al. (1998). Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable. Biochemistry, 37, 6958-6966. PubMed id: 9578582 DOI: 10.1021/bi972857n
Date:
25-Dec-97     Release date:   08-Apr-98    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P11540  (BARS_BACAM) -  Barstar from Bacillus amyloliquefaciens
Seq:
Struc: 		90 a.a.
89 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1021/bi972857n Biochemistry 37:6958-6966 (1998)
PubMed id: 9578582  
 
 
Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable.
G.S.Ratnaparkhi, S.Ramachandran, J.B.Udgaonkar, R.Varadarajan.
 
  ABSTRACT  
 
The crystal structure of the C82A mutant of barstar, the intracellular inhibitor of the Bacillus amyloliquefaciens ribonuclease barnase, has been solved to a resolution of 2.8 A. The molecule crystallizes in the space group I41 with a dimer in the asymmetric unit. An identical barstar dimer is also found in the crystal structure of the barnase-barstar complex. This structure of uncomplexed barstar is compared to the structure of barstar bound to barnase and also to the structure of barstar solved using NMR. The free structure is similar to the bound state, and there are no significant main-chain differences in the 27-44 region involved in barstar binding to barnase. The C82A structure shows significant differences from the average NMR structure, both overall and in the binding region. In contrast to the crystal structure, the NMR structure shows an unusually high packing value based on the occluded surface algorithm, indicating errors in the packing of the structure. We show that the NMR structures of homologous proteins generally show large differences in packing value, while the crystal structures of such proteins have very similar packing values, suggesting that protein packing density is not well determined by NMR.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17729269 A.May, and M.Zacharias (2008).
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking.
  Proteins, 70, 794-809.  
18441234 Y.Urakubo, T.Ikura, and N.Ito (2008).
Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation.
  Protein Sci, 17, 1055-1065.
PDB code: 2za4
17510956 D.Seeliger, and B.L.de Groot (2007).
Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps.
  Proteins, 68, 595-601.  
15647507 S.Chakravarty, L.Wang, and R.Sanchez (2005).
Accuracy of structure-derived properties in simple comparative models of protein structures.
  Nucleic Acids Res, 33, 244-259.  
15133161 C.Venclovas, K.Ginalski, and C.Kang (2004).
Sequence-structure mapping errors in the PDB: OB-fold domains.
  Protein Sci, 13, 1594-1602.
PDB code: 1s3o
12945054 H.Fan, and A.E.Mark (2003).
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
  Proteins, 53, 111-120.  
11266622 L.P.Lee, and B.Tidor (2001).
Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex.
  Protein Sci, 10, 362-377.  
11329282 S.J.Demarest, S.Q.Zhou, J.Robblee, R.Fairman, B.Chu, and D.P.Raleigh (2001).
A comparative study of peptide models of the alpha-domain of alpha-lactalbumin, lysozyme, and alpha-lactalbumin/lysozyme chimeras allows the elucidation of critical factors that contribute to the ability to form stable partially folded states.
  Biochemistry, 40, 2138-2147.  
11567104 X.J.Morelli, P.N.Palma, F.Guerlesquin, and A.C.Rigby (2001).
A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
  Protein Sci, 10, 2131-2137.  
10737939 D.W.Ritchie, and G.J.Kemp (2000).
Protein docking using spherical polar Fourier correlations.
  Proteins, 39, 178-194.  
9818269 R.A.Laskowski, M.W.MacArthur, and J.M.Thornton (1998).
Validation of protein models derived from experiment.
  Curr Opin Struct Biol, 8, 631-639.  
9772175 V.G.Panse, J.B.Udgaonkar, and R.Varadarajan (1998).
SecB binds only to a late native-like intermediate in the folding pathway of barstar and not to the unfolded state.
  Biochemistry, 37, 14477-14483.  
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.

 

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