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Newsletter No. 319
September 7, 2015

ACA News, IUCr Newsletter, IUCr Meetings List

AUGUST 2015 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Shabalin I, Dauter Z, Jaskolski M, Minor W, Wlodawer A. Crystallography and
chemistry should always go together: a cautionary tale of protein complexes with
cisplatin and carboplatin.
Acta Crystallogr D Biol Crystallogr. 2015 Sep 1;71(Pt
9):1965-79. doi: 10.1107/S139900471500629X. PubMed PMID: 26327386.

2: Venditti V, Schwieters CD, Grishaev A, Clore GM. Dynamic equilibrium between
closed and partially closed states of the bacterial Enzyme I unveiled by solution
NMR and X-ray scattering.
Proc Natl Acad Sci U S A. 2015 Aug 24. pii: 201515366.
[Epub ahead of print] PubMed PMID: 26305976.

3: Kirby TW, Gassman NR, Smith CE, Pedersen LC, Gabel SA, Sobhany M, Wilson SH,
London RE. Nuclear Localization of the DNA Repair Scaffold XRCC1: Uncovering the
Functional Role of a Bipartite NLS.
Sci Rep. 2015 Aug 25;5:13405. doi:
10.1038/srep13405. PubMed PMID: 26304019.

4: Zhao BM, Keasey SL, Tropea JE, Lountos GT, Dyas BK, Cherry S, Raran-Kurussi S,
Waugh DS, Ulrich RG. Phosphotyrosine Substrate Sequence Motifs for Dual
Specificity Phosphatases.
PLoS One. 2015 Aug 24;10(8):e0134984. doi:
10.1371/journal.pone.0134984. eCollection 2015. PubMed PMID: 26302245.

5: Curreli F, Kwon YD, Zhang H, Scacalossi D, Belov DS, Tikhonov AA, Andreev IA,
Altieri A, Kurkin AV,
Kwong PD, Debnath AK. Structure-Based Design of a Small
Molecule CD4-Antagonist with Broad Spectrum Anti-HIV-1 Activity.
J Med Chem. 2015
Aug 28. [Epub ahead of print] PubMed PMID: 26301736.

6: Yassine HM, Boyington JC, McTamney PM, Wei CJ, Kanekiyo M, Kong WP, Gallagher
JR, Wang L, Zhang Y, Joyce MG, Lingwood D, Moin SM, Andersen H, Okuno Y, Rao SS,
Harris AK,
Kwong PD, Mascola JR, Nabel GJ, Graham BS. Hemagglutinin-stem
nanoparticles generate heterosubtypic influenza protection.
Nat Med. 2015
Sep;21(9):1065-1070. doi: 10.1038/nm.3927. PubMed PMID: 26301691.

7: Jones CP, Ferré-D'Amaré AR. Recognition of the bacterial alarmone ZMP through
long-distance association of two RNA subdomains.
Nat Struct Mol Biol. 2015
Sep;22(9):679-85. doi: 10.1038/nsmb.3073. PubMed PMID: 26280533.

8: Vrentas C, Ghirlando R, Keefer A, Hu Z, Tomczak A, Gittis AG, Murthi A,
Garboczi DN, Gottesman S, Leppla SH. Hfqs in Bacillus anthracis: Role of protein
sequence variation in the structure and function of proteins in the Hfq family.

Protein Sci. 2015 Aug 14. doi: 10.1002/pro.2773. [Epub ahead of print] PubMed
PMID: 26271475.

9: Louis JM, Deshmukh L, Sayer JM, Aniana A,
Clore GM. Mutations Proximal to
Sites of Autoproteolysis and the α-Helix That Co-evolve under Drug Pressure
Modulate the Autoprocessing and Vitality of HIV-1 Protease.
Biochemistry. 2015
Aug 21. [Epub ahead of print] PubMed PMID: 26266692.

10: Jaskolski M, Miller M, Mohana Rao JK, Gustchina A,
Wlodawer A. Elucidation of
the structure of retroviral proteases: a reminiscence.
FEBS J. 2015 Aug 10. doi:
10.1111/febs.13397. [Epub ahead of print] PubMed PMID: 26258480.

11: Zhou D, Hansen D, Shabalin IG, Gustchina A, Vieira DF, de Brito MV, Araújo
AP, Oliva ML,
Wlodawer A. Structure of BbKI, a disulfide-free plasma kallikrein
inhibitor.
Acta Crystallogr F Struct Biol Commun. 2015 Aug 1;71(Pt 8):1055-62.
doi: 10.1107/S2053230X15011127. Epub 2015 Jul 29. PubMed PMID: 26249699; PubMed
Central PMCID: PMC4528941.

12: Pletnev VZ, Pletneva NV, Sarkisyan KS, Mishin AS, Lukyanov KA, Goryacheva EA,
Ziganshin RH,
Dauter Z, Pletnev S. Structure of the green fluorescent protein
NowGFP with an anionic tryptophan-based chromophore.
Acta Crystallogr D Biol
Crystallogr. 2015 Aug 1;71(Pt 8):1699-707. doi: 10.1107/S1399004715010159. Epub
2015 Jul 31. PubMed PMID: 26249350; PubMed Central PMCID: PMC4528802.

13: Fedeles BI, Freudenthal BD, Yau E, Singh V, Chang SC, Li D, Delaney JC,
Wilson SH, Essigmann JM. Intrinsic mutagenic properties of 5-chlorocytosine: A
mechanistic connection between chronic inflammation and cancer.
Proc Natl Acad
Sci U S A. 2015 Aug 18;112(33):E4571-80. doi: 10.1073/pnas.1507709112. Epub 2015
Aug 4. PubMed PMID: 26243878; PubMed Central PMCID: PMC4547254.

14: Kakar S, Fang X, Lubkowska L, Zhou YN, Shaw GX, Wang YX, Jin DJ, Kashlev M,
Ji X. Allosteric Activation of Bacterial Swi2/Snf2 Protein RapA by RNA
Polymerase: Biochemical and Structural Studies.
J Biol Chem. 2015 Aug 13. pii:
jbc.M114.618801. [Epub ahead of print] PubMed PMID: 26272746.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS AND TRICKS - Alternative Reservoirs in Vapor Diffusion Experiments
(Click for PDF reader to view articles)

At the 45th Mid-Atlantic Protein Crystallography Meeting, Dr. Ivan Shabalin from Professor Wladek Minor's laboratory at the University of Virginia shared various tricks in crystallization with the audience, including alterntive reservoirs in vapor diffusion experiments. Wondering what it is? Follow this link for an introduction.

ARCHIVE: Introduction, Pre-crystallization, Crystallization, Post-crystallization, Derivatization, Cryoprotection, Diffraction, Symmetry, Structure Solution, Structure Refinement, Structure Analysis & Presentation.

TOPIC DISCUSSION - Suggestions?

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, Structural Genomics, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and Publication.

LECTURES AND TUTORIALS - Dr. Dauter's Lectures Are Back!

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"


RIGAKU WEBINAR SERIES (2009 - PRESENT)

LOW RESOLUTION PHASING AND REFINEMENT (2011)

CRYSTALLOGRAPHY: SEEING THINGS IN A DIFFERENT LIGHT (2013)

CRYSTALLOGRAPHY: FOR ASPIRING CRYSTALLOGRAPHERS (2013)

 STRUCTURE FACTOR TUTORIAL (2014)

DATA COLLECTION FOR STRUCTURE DETERMENATION (2014)

ACHESYM: AN ALGORITHM AND SERVER FOR STANDARDIZED PLACEMENT OF MACROMOLECULAR MODELS IN THE UNIT CELL (2014)

NATIVE SAD IS MATURING (2015)

 LINKS - Suggestions?     

Databases: BMCD, CryoD, DisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry Database, Scattering

Programs: CCP4, COOT, DSSR, HKLPHENIX, PyMOL, SOLVE, USF, XDS


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, PhyreProbity, Protein, Robetta Fragment & HHpred  

Facilities: 
APS SER-CAT, APS SAXS Capabilities

 
Copyright © NIH X-Ray Diffraction Group                       Maintained by Dr. Xinhua Ji
on the NIH-NCI-CCR-MCL server (http://mcl1.ncifcrf.gov)