Newsletter 125
July 3, 2006

Item 1: June 2006 Publications by Members:

1:  Gan J, Gu Y, Li Y, Yan H, Ji X.
  Crystal structure of Mycobacterium tuberculosis shikinate kinase in complex with 
shikimic acid and and ATP analogue.
Biochemistry 2006 Jun 21; Abstract
   
2:  Wally J, Halbrooks PJ, Vonrhein C, Rould MA, Everse SJ, Mason AB, Buchanan SK. 
 The crystal structure of iron-free human serum transferrin provides insight into inter-lobe 
communication and receptor binding.
J Biol Chem. 2006 Jun 22; PMID: 16793765
   
3:  Kim IW, Peng XH, Sauna ZE, Fitzgerald PC, Xia D, Muller M, Nandigama K,
Ambudkar SV. 
 The Conserved Tyrosine Residues 401 and 1044 in ATP Sites of Human P-Glycoprotein 
Are Critical for ATP Binding and Hydrolysis: Evidence for aConserved Subdomain, the 
A-Loop in the ATP-Binding Cassette.
Biochemistry. 2006 Jun 20;45(24):7605-16. PMID: 16768456 
   
4:  Sun PD. 
 Human CD23: is it a lectin in disguise?
Structure. 2006 Jun;14(6):950-1. No abstract available. PMID: 16765887
   
5:  Prasanna MD, Vondrasek J, Wlodawer A, Rodriguez H, Bhat TN. 
 Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based
search engine for browsing compounds.
Proteins. 2006 Jun 1;63(4):907-17. PMID: 16508960

Item 2: Tips and Tricks - Crystallization

Crystallization of Protein-Protein Complexes
Peter D. Sun
LI, NIAID, NIH

As crystallographers zest for larger and larger molecular machinery (spoiled public is part to blame), what used to be a novelty: crystallization of protein-protein complexes, has indeed become a way of life for most of us. Like everyone else, our lab often struggles to obtain that elusive crystal of so-and-so complex. Over the years, it became clear to us that protein complexes often favored certain conditions of crystallizations. Although they were not as well defined as DNA-protein complex crystallizations, these conditions appeared more narrowly distributed than those for general soluble proteins. This lead us to conduct a survey on protein-protein complex crystallizations a few years ago, which resulted in a 48-condition sparse matrix screening kit. More recently, we revisited the survey using a much larger database of published structures and expanded the initial 48-condition to a 96-condition sparse matrix kit (Radaev, Li, and Sun, Acta Cryst. D62:605-612).

Click for Introduction and tips and tricks in Crystallization, Post-crystallization treatments for improving diffraction quality of protein crystals, Derivatization, Diffraction, Symmetry, Structure Solution, Structure Refinement, and Structure Analysis.

Item 3: Topic Discussion - Low Resolution Crystallography

Low Resolution Crystallography in the Hurley lab
James Hurley
LMB, NIDDK, NIH

I recently had a visiting seminar speaker in my office, and was describing some of the new structures in the lab to him. I was excited at the time to have the structure of a biggish multiprotein complex and another biggish full-length mammalian signaling protein to show off. The resolution was low in both cases, but for the biological questions being asked about how domains and subunits interacted, the structures were still informative. My visitor commented that “Your lab seems to have a real problem with resolution.” We have had a recent run of low resolution structures, whether due to bad luck, an increased focus on larger proteins and complexes, or both. (Click for the entire article)

Click for previous discussions on: PHASER, HKL2000, Parallel Protein Expression, Structural Genomics, NCS, Missing Atoms, Trends in Crystallography, and Absorption Correction.

2005)

Part 1: "How to read international tables?"

Part 2: "Data collection strategy" and "Twinning"

"Phasing methods - a general introduction to all methods"

Part 3: "SAD phasing, Quick halide soaking, and Radiation damage

with possible use of it for phasing"

This site is maintained by Dr. Xinhua Ji (jix@ncifcrf.gov) on the NCI-CCR-MCL server (http://mcl1.ncifcrf.gov).