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PDBsum entry 1yyf

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protein ligands Protein-protein interface(s) links
Chaperone/hydrolase PDB id
1yyf
Jmol
Contents
Protein chains
408 a.a. *
180 a.a. *
Ligands
ADP ×2
* Residue conservation analysis
PDB id:
1yyf
Name: Chaperone/hydrolase
Title: Correction of x-ray intensities from an hslv-hslu co- crystal containing lattice translocation defects
Structure: Atp-dependent hsl protease atp-binding subunit hslu. Chain: a, b. Synonym: heat shock protein hslu. Engineered: yes. Atp-dependent protease hslv. Chain: d, c. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: hslu, htpi. Expressed in: escherichia coli. Expression_system_taxid: 562. Bacillus subtilis. Organism_taxid: 1423. Gene: hslv, clpq, codw. Expression_system_taxid: 562
Biol. unit: Dodecamer (from PDB file)
Resolution:
4.16Å     R-factor:   0.280     R-free:   0.346
Authors: J.Wang,S.H.Rho,H.H.Park,S.H.Eom
Key ref:
J.Wang et al. (2005). Correction of X-ray intensities from an HslV-HslU co-crystal containing lattice-translocation defects. Acta Crystallogr D Biol Crystallogr, 61, 932-941. PubMed id: 15983416 DOI: 10.1107/S0907444905009546
Date:
24-Feb-05     Release date:   12-Jul-05    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A6H5  (HSLU_ECOLI) -  ATP-dependent protease ATPase subunit HslU
Seq:
Struc:
443 a.a.
408 a.a.
Protein chains
Pfam   ArchSchema ?
P39070  (CLPQ_BACSU) -  ATP-dependent protease subunit ClpQ
Seq:
Struc:
181 a.a.
180 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     response to stress   7 terms 
  Biochemical function     nucleotide binding     12 terms  

 

 
DOI no: 10.1107/S0907444905009546 Acta Crystallogr D Biol Crystallogr 61:932-941 (2005)
PubMed id: 15983416  
 
 
Correction of X-ray intensities from an HslV-HslU co-crystal containing lattice-translocation defects.
J.Wang, S.H.Rho, H.H.Park, S.H.Eom.
 
  ABSTRACT  
 
Because of lattice-translocation defects, two identical but translated lattices can coexist as a single coherent mosaic block in a crystal. The observed structure in such cases is a weighted sum of two identical but translated structures, one from each lattice; the observed structure factors are a weighted vector sum of the structure factors with identical unit amplitudes but shifted phases. The correction of X-ray intensities from a single crystal containing these defects of the hybrid HslV-HslU complex, which consists of Escherichia coli HslU and Bacillus subtilis HslV (also known as CodW), is reported. When intensities are not corrected, a biologically irrelevant complex (with CodW from one lattice and HslU from another) is implied to exist. Only upon correction does a biologically functional CodW-HslU complex structure emerge.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Observed alternating sharp-diffuse reflections. In the l direction, strong reflections are observed beyond 4.0 (large concentral circles) and some reflections are observed at 3.6 (reflections with small circles); in the h and k directions reflections barely pass 4.5 . Only the third of the reflections with index l = 3n (boxed) have typical Bragg spots and the remaining reflections have streaky features along the l direction. Data were processed to 4.16 , slightly below an ice ring at 4.15 .
Figure 6.
Figure 6 Incorrect model containing an extra HslV particle (magenta) at (0, 0, 1/3) fits the uncorrected observed data better than the correct model.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 932-941) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21231967 W.Wu, K.T.Park, T.Holyoak, and J.Lutkenhaus (2011).
Determination of the structure of the MinD-ATP complex reveals the orientation of MinD on the membrane and the relative location of the binding sites for MinE and MinC.
  Mol Microbiol, 79, 1515-1528.
PDB code: 3q9l
17979190 S.H.Rho, H.H.Park, G.B.Kang, Y.J.Im, M.S.Kang, B.K.Lim, I.S.Seong, J.Seol, C.H.Chung, J.Wang, and S.H.Eom (2008).
Crystal structure of Bacillus subtilis CodW, a noncanonical HslV-like peptidase with an impaired catalytic apparatus.
  Proteins, 71, 1020-1026.
PDB codes: 2z3a 2z3b
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.