Newsletter 104
September 12, 2005


The NIH X-Ray Diffraction Interest Group

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

Item 1: August 2005 Publications by Members:
 

1:  Burgess BR, Schuck P, Garboczi DN.
Dissection of merozoite surface protein 3, a representative of a family of
plasmodium falciparum surface proteins, reveals an oligomeric and highly
elongated molecule.
J Biol Chem. 2005 Aug 31; PMID: 16135515

2:  Ramagopal UA, Dauter Z, Thirumuruhan R, Fedorov E, Almo SC.
Radiation-induced site-specific damage of mercury derivatives: phasing and implications.
Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1289-98. Epub 2005 Aug 16. PMID: 16131763

3:  Vaisman A, Ling H, Woodgate R, Yang W.
Fidelity of Dpo4: effect of metal ions, nucleotide selection and
pyrophosphorolysis.
EMBO J. 2005 Sep 7;24(17):2957-67. PMID: 16107880

4:  Wlodawer A.
Giving credit where credit is due.
Nat Struct Mol Biol. 2005 Aug;12(8):634. PMID: 16077721

5:  Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T, Patel DJ.
Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided
endoribonuclease, provides insights into RISC-mediated mRNA cleavage.
Mol Cell. 2005 Aug 5;19(3):405-19. PMID: 16061186

6:  Bell JK, Botos I, Hall PR, Askins J, Shiloach J, Segal DM, Davies DR.
The molecular structure of the Toll-like receptor 3 ligand-binding domain.
Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10976-80. Epub 2005 Jul 25. PMID: 16043704

7:  Hickman AB, Perez ZN, Zhou L, Musingarimi P, Ghirlando R, Hinshaw JE, Craig NL, Dyda F.
Molecular architecture of a eukaryotic DNA transposase.
Nat Struct Mol Biol. 2005 Aug;12(8):715-21. PMID: 16041385

8:  Pancera M, Lebowitz J, Schon A, Zhu P, Freire E, Kwong PD, Roux KH, Sodroski J, Wyatt R.
Soluble mimetics of human immunodeficiency virus type 1 viral spikes produced by replacement of the native trimerization domain with a heterologous trimerization motif: characterization and ligand binding analysis.
J Virol. 2005 Aug;79(15):9954-69. PMID: 16014956

9:  Botos I, Melnikov EE, Cherry S, Kozlov S, Makhovskaya OV, Tropea JE, Gustchina A, Rotanova TV, Wlodawer A.
Atomic-resolution crystal structure of the proteolytic domain of Archaeoglobus fulgidus lon reveals the conformational variability in the active sites of lon proteases.
J Mol Biol. 2005 Aug 5;351(1):144-57. PMID: 16002085

10:  Williams DC Jr, Lee JY, Cai M, Bewley CA, Clore GM.
Crystal structures of the HIV-1 inhibitory cyanobacterial protein MVL free and bound to Man3GlcNAc2: structural basis for specificity and high-affinity binding to the core pentasaccharide from n-linked oligomannoside.
J Biol Chem. 2005 Aug 12;280(32):29269-76. PMID: 15937331

Item 2: Tips and Tricks

This section is always open for contributions. Click for Introduction and tips and tricks in Crystallization, Derivatization, Diffraction, Symmetry, Structure Solution, Structure Refinement, and Structure Analysis.

 

Item 3: Topic Discussion

PHASER: MR with Maximum Likelihood

Dr. Mark Mayer (NICHD): Keeping up with new software is time consuming especially for small labs. The NIH X-Ray Diffraction Interest Group News Letter gives us a chance as a community to share information about newer programs, and tips for using them. On the Mac side of things the Structural Biology Grid has version of CNS and Refmac that support multithreading and fast FFT calculations on G4/G5 systems which significantly speed up calculation of composite omit maps. The binaries are available from: http://www.sbgrid.org/osx.php?software=1&id=0

A relatively new Molecular Replacement program PHASER has just been updated to version 1.3.1 and appears to be a very useful tool.

PHASER was written by Randy Read, Ralf Grosse-Kunstleve and colleagues as part of PHENIX and is available from: http://www-structmed.cimr.cam.ac.uk/phaser/.

Binaries are available for multiple platforms including Mac OsX, linux, SGIs, and PCs. An interface to CCP4i is also available. Eventually the program will be incorporated into the CCP4 suite.

Among many nice features are use of maximum likelihood targets; anisotropy correction; a very user friendly interface when run from CCP4i; Z scoring as an indication of the success of the fit; automatic testing of enantiomorphic space groups; the ability to use an ensemble of models as targets; and the ability to search for and fit domains independently. The latter feature was attractive to me in the case of a 2.2-angstrom data set from my home facility (P41212 or P43212) for which I was expecting a large conformational change from my search model. PHASER identified the space group and found the two domains in their new orientations without intervention.

The program has many features I have not tried which extend those available in MOLREP and AmoRe.

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

 

Item 4: Lectures

Dr. Zbigniew Dauter's Lectures at the NIH (03/29-31)

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"

 
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