PDBsum entry 2e6u

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Structural genomics, unknown function PDB id
Protein chain
142 a.a. *
_CL ×3
Waters ×45
* Residue conservation analysis
PDB id:
Name: Structural genomics, unknown function
Title: Crystal structure of hypothetical protein ph1109 from pyroco horikoshii
Structure: Hypothetical protein ph1109. Chain: x. Engineered: yes
Source: Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Gene: ph1109. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.80Å     R-factor:   0.207     R-free:   0.233
Authors: Y.Kitago,Y.Min,N.Watanabe,I.Tanaka
Key ref:
Y.Kitago et al. (2005). Structure determination of a novel protein by sulfur SAD using chromium radiation in combination with a new crystal-mounting method. Acta Crystallogr D Biol Crystallogr, 61, 1013-1021. PubMed id: 16041065 DOI: 10.1107/S0907444905012734
03-Jan-07     Release date:   23-Jan-07    
Supersedes: 2czz
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O58836  (O58836_PYRHO) -  Putative uncharacterized protein PH1109
144 a.a.
142 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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


DOI no: 10.1107/S0907444905012734 Acta Crystallogr D Biol Crystallogr 61:1013-1021 (2005)
PubMed id: 16041065  
Structure determination of a novel protein by sulfur SAD using chromium radiation in combination with a new crystal-mounting method.
Y.Kitago, N.Watanabe, I.Tanaka.
A novel and easy crystal-mounting technique was developed for the sulfur SAD method using Cr Kalpha radiation (2.29 A). Using this technique, the cryo-buffer and cryoloop around the protein crystal can be removed before data collection in order to eliminate their X-ray absorption. The superiority and reproducibility of the data sets with this mounting technique were demonstrated using tetragonal hen egg-white lysozyme crystals. The structure of a novel protein, PH1109, from Pyrococcus horikoshii OT3 was solved using this technique. At the wavelength of Cr Kalpha radiation, the anomalous signal |DeltaF|/|F| of PH1109 is expected to be 1.72% as this protein of 144 residues includes four methionines and two cysteines. Sulfur SAD phasing was performed using SHELXD and SHELXE. In the case of the data set obtained using this novel crystal-mounting technique, 54.9% of all residues were built with side chains automatically by RESOLVE. On the other hand, only 16.0% were built with side chains for the data set collected using the standard cryoloop. These results indicated that this crystal-mounting technique was superior to the standard loop-mounting method for the measurement of small anomalous differences at longer wavelength and yielded better results in sulfur-substructure solution and initial phasing. The present study demonstrates that the sulfur SAD method with a chromium source becomes enhanced and more practical for macromolecular structure determination using the new crystal-mounting technique.
  Selected figure(s)  
Figure 1.
Figure 1 (a) A schematic illustration of the novel mounting technique. (i) Picking up a protein crystal using a nylon loop at the top of glass micropipette and mounting the tools on the goniometer head intercepting the cryostream. (ii) Aspirating the cryo-buffer through the micropipette and flushing with the cold nitrogen stream. (iii) Removing the nylon loop under cryo-conditions. (b) The mounting base for the novel mounting technique. This tool can hold the micropipette and aspirate the cryo-buffer through the flexible tube. (c) Left, the tip of the micropipette and nylon loop before picking up a protein crystal. The nylon loop was glued to the tip of the micropipette. Middle, the tip of the micropipette and a protein crystal after aspirating the cryo-buffer and freezing. Right, the tip of the micropipette and a protein crystal after removing the nylon loop. In the middle and right pictures, a thaumatin (Sigma T-7638) crystal was used as the sample.
Figure 5.
Figure 5 (a) Overview of the initial model of PH1109 built by RESOLVE using the data set from our crystal-mounting method. The model identified without side chains is shown in red and that with side chains is shown in blue. (b) The final model constructed by Lafire. (c) The initial model produced from the data set obtained using the standard cryoloop built by RESOLVE. The colours are the same as in (a). (d) The initial model produced using an extracted data set that has only the same reflections as the data set with the standard loop.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1013-1021) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20029111 J.Brandao-Neto, S.P.Thompson, A.R.Lennie, F.F.Ferreira, and C.C.Tang (2010).
Characterization of wax as a potential diffraction intensity standard for macromolecular crystallography beamlines.
  J Synchrotron Radiat, 17, 53-60.  
18981178 M.Kitamura, M.Okuyama, F.Tanzawa, H.Mori, Y.Kitago, N.Watanabe, A.Kimura, I.Tanaka, and M.Yao (2008).
Structural and Functional Analysis of a Glycoside Hydrolase Family 97 Enzyme from Bacteroides thetaiotaomicron.
  J Biol Chem, 283, 36328-36337.
PDB codes: 2d73 2zq0
17342453 T.B.Hiyama, M.Zhao, Y.Kitago, M.Yao, S.Sekine, T.Terada, C.Kuroishi, Z.J.Liu, J.P.Rose, S.Kuramitsu, M.Shirouzu, N.Watanabe, S.Yokoyama, I.Tanaka, and B.C.Wang (2006).
Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins.
  J Struct Funct Genomics, 7, 119-129.
PDB codes: 2d59 2d5a
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