Newsletter 143
March 12, 2007


The NIH X-Ray Diffraction Interest Group

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

The 4th annual SER-CAT Symposium 16 March 2007, National Cancer Institute at Frederick, Frederick, MD, USA

The 37th Mid-Atlantic Macromolecular Crystallography Meeting (June 7-9, 2007) will be hosted by the University of Virginia.

The 2007 Meeting of the American Crystallographic Associstion 21-26 July 2007, Salt Lake City, UT, USA

The 9th International Conference on Biology and Synchrotron Radiation 13-17 August 2007, Manchester, England


Item 1: February 2007 Publications by Members:

1:  Blaszczyk J, Li Y, Gan J, Yan H, Ji X. 
Structural Basis for the Aldolase and Epimerase Activities of Staphylococcus
aureus Dihydroneopterin Aldolase.
J Mol Biol. 2007 Feb 9; [Epub ahead of print] PMID: 17331536

2: Wlodawer A.
Deposition of structural data redux.
Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):421-3. Epub 2007 Feb 21.
No abstract available. PMID: 17327681

3: Dauter Z, Baker T.
Numerology.
Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):275. Epub 2007 Feb 21. No
abstract available. PMID: 17327662

4: Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, Xiang SH, Yang X, Zhang MY,
Zwick MB, Arthos J, Burton DR, Dimitrov DS, Sodroski J, Wyatt R, Nabel GJ, Kwong
PD
.
Structural definition of a conserved neutralization epitope on HIV-1 gp120.
Nature. 2007 Feb 15;445(7129):732-7. PMID: 17301785

5: Iwahara J, Jung YS, Clore GM.
Heteronuclear NMR Spectroscopy for Lysine NH(3) Groups in Proteins: Unique
Effect of Water Exchange on (15)N Transverse Relaxation.
J Am Chem Soc. 2007 Mar 14;129(10):2971-80. Epub 2007 Feb 15. PMID: 17300195

6: Horton JK, Stefanick DF, Kedar PS, Wilson SH.
ATR signaling mediates an S-phase checkpoint after inhibition of
poly(ADP-ribose) polymerase activity.
DNA Repair (Amst). 2007 Feb 8; [Epub ahead of print] PMID: 17292679

7: Lee S, Joshi A, Nagashima K, Freed EO, Hurley JH.
Structural basis for viral late-domain binding to Alix.
Nat Struct Mol Biol. 2007 Mar;14(3):194-9. Epub 2007 Feb 4. PMID: 17277784

8: Schwieters CD, Clore GM.
A physical picture of atomic motions within the Dickerson DNA dodecamer in
solution derived from joint ensemble refinement against NMR and large-angle
X-ray scattering data.
Biochemistry. 2007 Feb 6;46(5):1152-66. PMID: 17260945

Item 2: Tips and Tricks

Wei Yang (NIDDK): Crystallization of Protein-DNA Complexes (updated)
    Macromolecular interaction is essential, necessary and unavoidable in a living organism. Specific interactions among macromolecules are required for molecular machinery assembly and for progression and regulation of metabolic reactions.  To fully understand a biological process, it is essential to determine the atomic structures of and interactions among components of a macromolecular complex and to decipher how these structures and interactions change during a reaction or signaling cycle.  Some macromolecular complexes are naturally stable, for example tetrameric hemoglobin, nucleosome, and ribosome. But most macromolecular complexes are formed only transiently, e.g. an enzyme and substrate complex, a growth factor and its receptor interaction, or transcription factors assembled on a promoter.  To determine structures of macromolecular complexes, whether stable or transient, has become a common practice of structural biologists in the 21st century. (Full Article)


Click for
Introduction and tips and tricks in
Pre-crystallization modification, Crystallization, Post-crystallization treatment, Derivatization, Diffraction, Symmetry, Structure Solution, Structure Refinement, and Structure Analysis.

Item 3: Topic Discussion

Click for previous discussions on: 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 (03/29-31/2005)

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).