Newsletter 91
March 14, 2005


The NIH X-Ray Diffraction Interest Group

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

Dr. Wei Yang (NIDDK):

        Dr. Zbigniew Dauter has graciously agreed to present a series of 8 lectures on crystal symmetry, twinning, data collection, and phasing by various methods at the end of this month. The lectures will be given on the main campus of NIH, in Building 5 Room 127, and the schedule of his lectures is as following.
 

March 29 (Tuesday), 4-7 pm, "How to read international tables?"

March 30 (Wednesday) 3-5:30 pm, "Data collection strategy" and "Twinning"

March 30 (Wednesday) 7:30-8:30 pm, "Phasing methods - a general introduction to all methods"

March 31 (Thursday) 9:30-12:30, "SAD phasing, Quick halide soaking, and Radiation damage with possible use of it for phasing"

 
        The lecture times are selected based on the room availability. We have some flexibility but not much.  Everyone including PIs, postdocs, technicians and students is welcome.
        To have an idea of the size of audience, I would like to ask you email me yangwei@helix.nih.gov if you plan to attend one or more sessions of the lectures.
 

Item 1: February 2005 Publications by Members:

 

1:  Hansen AM, Gu Y, Li M, Andrykovitch M, Waugh DS, Jin DJ, Ji X.
Structural basis for the function of stringent starvation protein A as a transcription factor.
J Biol Chem. 2005 Feb 25; PMID: 15735307

2:  Shi D, Morizono H, Yu X, Roth L, Caldovic L, Allewell NM, Malamy MH, Tuchman M.
Crystal structure of N-acetylornithine transcarbamylase from Xanthomonas campestris: A novel enzyme in a new arginine biosynthetic pathway found in several eubacteria.
J Biol Chem. 2005 Feb 24; PMID: 15731101

3:  Kwong PD.
Human immunodeficiency virus: refolding the envelope.
Nature. 2005 Feb 24;433(7028):815-6. No abstract available.
PMID: 15729327

4:  Mayer ML.
Crystal Structures of the GluR5 and GluR6 Ligand Binding Cores: Molecular Mechanisms Underlying Kainate Receptor Selectivity.
Neuron. 2005 Feb 17;45(4):539-52. PMID: 15721240

5:  Hickman AB, Dyda F.
Binding and unwinding: SF3 viral helicases.
Curr Opin Struct Biol. 2005 Feb;15(1):77-85. PMID: 15718137

6:  Prag G, Lee S, Mattera R, Arighi CN, Beach BM, Bonifacino JS, Hurley JH.
Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, {gamma}-ear-containing, ADP-ribosylation-factor-binding proteins.
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2334-2339. PMID: 15701688

7:  Park H, Adsit FG, Boyington JC.
The 1.4 A crystal structure of the human oxidized low density lipoprotein receptor LOX-1.
J Biol Chem. 2005 Feb 5; PMID: 15695803

8:  Yang W.
Portraits of a Y-family DNA polymerase.
FEBS Lett. 2005 Feb 7;579(4):868-72. PMID: 15680965

9:  Gupta N, Arthos J, Khazanie P, Steenbeke TD, Censoplano NM, Chung EA, Cruz CC, Chaikin MA, Daucher M, Kottilil S, Mavilio D, Schuck P, Sun PD, Rabin RL, Radaev S, Van Ryk D, Cicala C, Fauci AS.
Targeted lysis of HIV-infected cells by natural killer cells armed and triggered by a recombinant immunoglobulin fusion protein: implications for immunotherapy.
Virology. 2005 Feb 20;332(2):491-7. PMID: 15680414

10:  Swales K, Kakizaki S, Yamamoto Y, Inoue K, Kobayashi K, Negishi M.
Novel CAR-mediated mechanism for synergistic activation of two distinct elements within the human cytochrome P450 2B6 gene in HepG2 cells.
J Biol Chem. 2005 Feb 4;280(5):3458-66. PMID: 15563456

11:  Yusof AM, Hu NJ, Wlodawer A, Hofmann A.
Structural evidence for variable oligomerization of the N-terminal domain of cyclase-associated protein (CAP).
Proteins. 2005 Feb 1;58(2):255-62. PMID: 15558566


Item 2: Tips and Tricks

Lothar Esser (NCI): The Successor of BEAST - Molecular replacement is always a bit tricky especially with poor data. The membrane protein that I work on provides only very anisotropic data and the only program that could handle it was the successor of BEAST: Phaser. So many people have said so many good things about phaser ( see G. Sheldrick's comments on the CCP4BB ) that I do not need to add anything only so much that it solved my difficult problem too. I have a solution despite less than ideal data. What usually convinces me of the correctness of a solution is when I see peaks in the anomalous difference map for sulfur atoms or atoms of which Z>=16. Just to be on the safe side, my MR models are usually free of S or any heavy atoms so that when I get peaks in the right places, I am convinced. Coming back to data, Phaser rejects outliers also but its great strength (at least in my case) lies in the correction of anisotropic data. I'd highly recommend it.

Xinhua Ji (NCI): The Beauty of BEAST - Outliers among diffraction data are usually of lower resolution and relatively stronger and thereby have greater impact on the functions derived from intensities. One consequence of this impact is the lack of phasing power of molecular replacement (MR) solution. We recently encountered this problem with an MR solution obtained using a search model equivalent to ~50% the structure. With AMoRe, we found an solution; but we were not able to complete the structure using either the difference Fourier synthesis or other programs. Assuming that the MR solution was not accurate, we tried MR again excluding potential outliers. BEAST identified 22 potential outliers and rejected them from likelihood calculations. The MR solution was outstanding and the difference map derived from the partial structure reveals the missing portion of the structure.

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

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

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