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PDBsum entry 1x6q

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protein links
Structural protein PDB id
1x6q
Jmol
Contents
Protein chain
120 a.a. *
Waters ×197
* Residue conservation analysis
PDB id:
1x6q
Name: Structural protein
Title: Structure 3: cryocooled crystal structure of the truncated pak pilin from pseudomonas aeruginosa at 1.51a resolution
Structure: Fimbrial protein. Chain: a. Synonym: pilin, strain pak. Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 287. Strain: k. Cellular_location: extracellular filamentous appendage. Gene: pila, fima. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Resolution:
1.51Å     R-factor:   0.139     R-free:   0.161
Authors: K.V.Dunlop,R.T.Irvin,B.Hazes
Key ref:
K.V.Dunlop et al. (2005). Pros and cons of cryocrystallography: should we also collect a room-temperature data set? Acta Crystallogr D Biol Crystallogr, 61, 80-87. PubMed id: 15608379 DOI: 10.1107/S0907444904027179
Date:
11-Aug-04     Release date:   19-Apr-05    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02973  (FMPA_PSEAI) -  Fimbrial protein
Seq:
Struc:
150 a.a.
120 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     pilus   1 term 
  Biological process     cell adhesion   1 term 

 

 
DOI no: 10.1107/S0907444904027179 Acta Crystallogr D Biol Crystallogr 61:80-87 (2005)
PubMed id: 15608379  
 
 
Pros and cons of cryocrystallography: should we also collect a room-temperature data set?
K.V.Dunlop, R.T.Irvin, B.Hazes.
 
  ABSTRACT  
 
High-resolution protein structures are becoming more common owing to the availability of increasingly brilliant synchrotron X-ray sources. However, to withstand the increased X-ray dose the crystals must be held at cryogenic temperatures. To compare the benefit of increased resolution with the drawback of potential temperature-induced changes, three room-temperature and three cryogenic data sets for PAK pilin have been collected at resolutions between 1.8 and 0.78 A. The results show that although the high-resolution cryogenic structures are more precise and more detailed, they also show systematic deviations from the room-temperature structures. Small but significant differences are even observed in the structural core, whilst more extensive changes occur at the protein surface. These differences can affect biological interpretations, especially because many important biological processes take place at the protein surface. Accordingly, although high-quality cryogenic synchrotron data is extremely valuable to protein crystallography, room-temperature structures are still desirable, especially if the research question involves protein features that are sensitive to temperature-induced changes.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 2F[o] - F[c] density for Glu27 contoured at 1 . Density for structure 3 (yellow) shows two Glu27 side-chain conformations. Density for structure 4 (green) shows only one side-chain conformation. Structures 3 and 4 are representative of all cryocooled and all room-temperature structures, respectively. The figure was produced using Xfit (McRee, 1999[McRee, D. E. (1999). J. Struct. Biol. 125, 156-165.]) and Raster3D (Merritt & Murphy, 1994[Merritt, E. A. & Murphy, M. E. P. (1994). Acta Cryst. D50, 869-873.]).
Figure 4.
Figure 4 Ball-and-stick model showing superimposed cryocooled (green) and room-temperature (dark blue) water molecules for all six PAK structures within a small section of the PAK protein. The structure shows that waters observed in room-temperature structures are also present in cryocooled structures but not vice versa. The figure was made using Xfit (McRee, 1999[McRee, D. E. (1999). J. Struct. Biol. 125, 156-165.]) and Raster3D (Merritt & Murphy, 1994[Merritt, E. A. & Murphy, M. E. P. (1994). Acta Cryst. D50, 869-873.]).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 80-87) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20382997 M.Weik, and J.P.Colletier (2010).
Temperature-dependent macromolecular X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 437-446.  
16604066 A.Y.Lyubimov, P.I.Lario, I.Moustafa, and A.Vrielink (2006).
Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment.
  Nat Chem Biol, 2, 259-264.
PDB codes: 1n4u 1n4v 1n4w 2gew
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