Newsletter 162
December 17, 2007


The NIH X-Ray Diffraction Interest Group

Newsletter web site: http://mcl1.ncifcrf.gov/nihxray

2008 Meeting of the American Crystallography Association
31 May - 5 June 2008, Knoxville, TN, USA

21st Congress of the International Union of Crystallography 2008
23 - 31 August 2008, Osaka, Japan

 

Item 1: November 2007 Publications by Members of the Group

1: Gan J, Shaw G, Tropea JE, Waugh DS, Court DL, Ji X.
A stepwise model for double-stranded RNA processing by
ribonuclease III. Mol Microbiol. 2007 Nov 27; PMID: 18047582

2: Esser L, Elberry M, Zhou F, Yu CA, Yu L, Xia D.
Inhibitor complexed structures of the cytochrome bc1 from
the photosynthetic bacterium Rhodobacter sphaeroides.
J Biol Chem. 2007 Nov 26; PMID: 18039651

3: Wlodawer A, Minor W, Dauter Z, Jaskolski M.
Protein crystallography for non-crystallographers, or how
to get the best (but not more) from published macromolecular
structures.
FEBS J. 2007 Nov 23; PMID: 18034855

4: Lindwasser OW, Smith WJ, Chaudhuri R, Yang P, Hurley JH,
Bonifacino JS.
A Diacidic Motif in HIV-1 Nef is a Novel Determinant of
Binding to AP2.
J Virol. 2007 Nov 21; PMID: 18032517

5: McKenna CE, Kashemirov BA, Upton TG, Batra VK, Goodman MF,
Pedersen LC, Beard WA, Wilson SH.
(R)-beta,gamma-Fluoromethylene-dGTP-DNA Ternary Complex with
DNA Polymerase beta.
J Am Chem Soc. 2007 Nov 22; PMID: 18031037

6: Ramón-Maiques S, Kuo AJ, Carney D, Matthews AG,
Oettinger MA, Gozani O, Yang W.
The plant homeodomain finger of RAG2 recognizes histone H3
methylated at both lysine-4 and arginine-2.
PNAS U S A. 2007 Nov 27;104(48):18993-8. PMID: 18025461

7: Blaszczyk J, Li Y, Cherry S, Alexandratos J, Wu Y, Shaw G,
Tropea JE, Waugh DS, Yan H, Ji X.
Structure and activity of Yersinia pestis 6-hydroxymethyl-
7,8-dihydropterin pyrophosphokinase as a novel target for the
development of antiplague therapeutics.
Acta Crystallogr D. 2007 Nov;63:1169-77. PMID: 18007032

8: McFeeters RL, Altieri AS, Cherry S, Tropea JE, Waugh DS,
Byrd RA.
The High-Precision Solution Structure of Yersinia Modulating
Protein YmoA Provides Insight into Interaction with H-NS.
Biochemistry. 2007 Nov 15; PMID: 18001134

9: Barnard TJ, Dautin N, Lukacik P, Bernstein HD, Buchanan SK.
Autotransporter structure reveals intra-barrel cleavage
followed by conformational changes.
Nat Struct Mol Biol. 2007 Nov 11; PMID: 17994105

10: Kodama S, Moore R, Yamamoto Y, Negishi M.
Human nuclear pregnane X receptor cross-talk with CREB to
repress cAMP activation of the glucose-6-phosphatase gene.
Biochem J. 2007 Nov 1;407(3):373-81. PMID: 17635106

Item 2: Tips and Tricks

Recommended viewing: How long will my crystal last?

Dr. Susan Buchanan (NIDDK): Crystallization of Integral Membrane Proteins
    X-ray crystallography has become a very powerful tool for determining the structures of integral membrane proteins, with almost 200 unique membrane protein structures solved as of December 2007 (for a complete list, see Stephen White’s summary at http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html). However, membrane protein structures still represent less than 1% of all structures in the PDB. The major bottlenecks in the field are the expression of sufficient quantities of functional membrane proteins and the growth of well ordered crystals for X-ray analysis. This short review covers only aspects pertaining to crystallization. Our approach to membrane protein crystallization was recently written up for Current Protocols in Protein Science (Unit 17.9, available from the NIH library website). An interesting review has been written by Patrick Loll1. (Full Article)

Item 3: Topic Discussion

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

 

Item 4: Dr. Zbigniew Dauter's Lectures at the NIH (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).