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Newsletter No. 399
June 3, 2019
Michael Rossmann, 88

ACA News, IUCr Newsletter, IUCr Meetings List

ACA 2019, FEBS 2019, Protein Society 2019

MAY 2019 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Sim MJW, Rajagopalan S, Altmann DM, Boyton RJ, Sun PD, Long EO. Human NK cell
receptor KIR2DS4 detects a conserved bacterial epitope presented by HLA-C
. Proc
Natl Acad Sci U S A. 2019 May 28. pii: 201903781. doi: 10.1073/pnas.1903781116.
[Epub ahead of print] PubMed PMID: 31138701.

2: Sekula B, Dauter Z. Spermidine Synthase (SPDS) Undergoes Concerted Structural
Rearrangements Upon Ligand Binding - A Case Study of the Two SPDS Isoforms From
Arabidopsis thaliana
. Front Plant Sci. 2019 May 7;10:555. doi:
10.3389/fpls.2019.00555. eCollection 2019. PubMed PMID: 31134111; PubMed Central
PMCID: PMC6514230.

3: Liu WC, Zhou F, Xia D, Shiloach J. Expression of multidrug transporter
P-glycoprotein in Pichia pastoris affects the host's methanol metabolism
. Microb
Biotechnol. 2019 May 26. doi: 10.1111/1751-7915.13420. [Epub ahead of print]
PubMed PMID: 31131547.

4: Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins AL, Olins DE,
Bai Y, Zhang
P
. Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided
by an antibody fragmen
t. Nat Commun. 2019 May 24;10(1):2301. doi:
10.1038/s41467-019-10247-4. PubMed PMID: 31127102.

5: Amano M, Salcedo-Gómez PM, Yedidi RS, Zhao R, Hayashi H, Hasegawa K, Nakamura
T, Martyr CD, Ghosh AK, Mitsuya H. Novel Central Nervous System (CNS)-Targeting
Protease Inhibitors for Drug-Resistant HIV Infection and HIV-Associated CNS
Complications
. Antimicrob Agents Chemother. 2019 May 6. pii: AAC.00466-19. doi:
10.1128/AAC.00466-19. [Epub ahead of print] PubMed PMID: 31061155.

6: Miller Jenkins LM, Paine EL, Deshmukh L, Nikolayevskiy H, Lyons GC, Scerba MT,
George Rosenker K, Luecke HF, Louis JM, Chertova E, Gorelick RJ, Ott DE, Clore
GM
, Appella DH. Inhibition of HIV Maturation via Selective Unfolding and
Cross-Linking of Gag Polyprotein by a Mercaptobenzamide Acetylator
. J Am Chem
Soc. 2019 May 13. doi: 10.1021/jacs.9b02743. [Epub ahead of print] PubMed PMID:
31042030.

7: Jin L, Song H, Tropea JE, Needle D, Waugh DS, Gu S, Ji X. The molecular
mechanism of dsRNA processing by a bacterial Dicer
. Nucleic Acids Res. 2019 May
21;47(9):4707-4720. doi: 10.1093/nar/gkz208. PubMed PMID: 30916338; PubMed
Central PMCID: PMC6511835.


For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - Date Collection with ID22 and Eiger16M

Fred Dyda (NIDDK): During a survey of data collection practices, it became apparent that most users do not take advantage of the current capabilities of ID22 and the Eiger16M. In particular it has been shown that excellent data can collected using 0.2 or 0.25 degrees / 0.05 sec speed so 200 degrees can be collected in 36 or 50 sec. One would of course have to increase transmission, but this should be possible as most people seem to collect at 80 or 90% attenuation. This should be OK, as all indicate that decay is dependent of totla accumulated does and is independent of dose rate.


Detergent-Free Membrane Protein System |  In a newly published paper in PNAS, a team led by Dr. Youzhong Guo of VCU's School of Pharmacy used a new detergent-free method that allowed them to examine the membrane of an Escherichia coli cell, with lipids still in place, providing the clearest view ever of cell membrane that yields unexpected structure. 

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

TOPIC DISCUSSIONSuggestions?

ARCHIVE: Test-set-and-R-free, Twinning, Low Resolution Crystallography, PHASER, HKL2000, Parallel Expression, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and PublicationValidation, Table 1.

LECTURES AND TUTORIALS - Data Collection Strategies

 The Fascinating World of Crystallography

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)

A GLIMPSE OF STRUCTURAL BIOLOGY THROUGH X-RAY CRYSTALLOGRAPHY (2014)

CRYSTAL CLEAR (2014)

NATIVE SAD IS MATURING (2015)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 LINKS - Suggestions?

Databases: BMCDDisProt, ExPASy, HAD, HIC-Up, Metal Sites, NDBPDB, PDBe
,
                 Protein Geometry, Scattering

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


Servers: ACHESYM,
Anisotropy, CheckMyMetal, Crystal, C6, Dali, DSSR, ESPript
              Grade, PDBePISA, Phyre, MolProbity, Protein, Robetta Fragment, HHpred,
 
            RestraintLib,


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 (https://mcl1.ncifcrf.gov)