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Newsletter No. 330
March 7, 2016

ACA News, IUCr Newsletter, IUCr Meetings List

FEBRUARY 2016 PUBLICATIONS BY MEMBERS OF THE GROUP  


1: Raczynska J,
Wlodawer A, Jaskolski M. Prior knowledge or freedom of
interpretation? A critical look at a recently published classification of "novel"
Zn binding sites
. Proteins. 2016 Feb 23. doi: 10.1002/prot.25024. [Epub ahead of
print] PubMed PMID: 26914344.

2: Ott de Bruin L, Yang W, Capuder K, Lee YN, Antolini M, Meyers R, Gellert M,
Musunuru K, Manis J, Notarangelo L. Rapid generation of novel models of RAG1
deficiency by CRISPR/Cas9-induced mutagenesis in murine zygotes
. Oncotarget. 2016
Feb 12. doi: 10.18632/oncotarget.7341. [Epub ahead of print] PubMed PMID:
26887046.

3: Hall TM. De-coding and re-coding RNA recognition by PUF and PPR repeat
proteins
. Curr Opin Struct Biol. 2016 Feb 11;36:116-121. doi:
10.1016/j.sbi.2016.01.010. [Epub ahead of print] Review. PubMed PMID: 26874972;
PubMed Central PMCID: PMC4757904.

4: Morozov GI, Zhao H, Mage MG, Boyd LF, Jiang J, Dolan MA, Venna R, Norcross MA,
McMurtrey CP, Hildebrand W, Schuck P, Natarajan K, Margulies DH. Interaction of
TAPBPR, a tapasin homolog, with MHC-I molecules promotes peptide editing
. Proc
Natl Acad Sci U S A. 2016 Feb 23;113(8):E1006-15. doi: 10.1073/pnas.1519894113.
Epub 2016 Feb 11. PubMed PMID: 26869717.

5: Minor W,
Dauter Z, Helliwell JR, Jaskolski M, Wlodawer A. Safeguarding
Structural Data Repositories against Bad Apples
. Structure. 2016 Feb
2;24(2):216-20. doi: 10.1016/j.str.2015.12.010. Review. PubMed PMID: 26840827;
PubMed Central PMCID: PMC4743038.

6: Pluchino KM, Hall MD, Moen JK, Chufan EE, Fetsch PA, Shukla S, Gill DR, Hyde
SC,
Xia D, Ambudkar SV, Gottesman MM. Human-Mouse Chimeras with Normal Expression
and Function Reveal That Major Domain Swapping Is Tolerated by P-Glycoprotein
(ABCB1)
. Biochemistry. 2016 Feb 23;55(7):1010-23. doi:
10.1021/acs.biochem.5b01064. Epub 2016 Feb 10. PubMed PMID: 26820614.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS AND METHODS - Widening the Reach of Structural Biology

Micro-electron diffraction (MicroED) data is collected from small 3D microcrystals  using a very low electron dose and readily processed using MOSFLM. Using the MicroED approach, the structure of lysozyme was solved using at 2.5-angstrom resolution (PDB entry 3J6K)  and  the structure of the toxic core of alpha-synuclein was determined at 1.4-angstrom resolution (PDB entry 4RIL). For a review, please see Protein structure determination by MicroED.

Cryo-electron microscopy (CryoEM) is an ensemble of techniques allowing the observation of biological specimens in their native environment at cryogenic temperatures in EM. For a recent cryoEM structure at high resolution, please see 2.2 Å resolution cryo-EM structure of b-galactosidase in complex with a cell-permeant inhibitor. For an overview, please see CryoEM at IUCrJ: a new era.

Small-angle X-ray scattering (SAXS) is capable of delivering structural information of biological macromolecules and their complexes in solution, small or large. For a recent example, the SAXS model for a ~500-kDa RapA:RNA polymerase complex (~230 angstroms in its longest dimension), please see Allosteric Activation of Bacterial Swi2/Snf2 Protein RapA by RNA Polymerase: Biochemical and Structural Studies.

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

TOPIC DISCUSSIONCrystal Structures

Mariusz Jaskolski: Pathological Behavior of Atomic Occupancy Factors
A number of PDB files have been detected and reported by Zbyszek Dauter, in which the atomic occupancy factors show a pathological behavior, where covalently connected atoms have uncorrelated fractional occupancies.  This pathology seems to have been spreading unnoticed because MR-generated structures inherited the pathology from some earlier models, and the refinement programs were not rigorous enough to block (or at least signal) the "infection".  You might be advised to check your PDB files for this pathology, using an ad-hoc server http://achesym.ibch.poznan.pl/occucheck/ by Marcin Kowiel.

Mariusz Jaskolski: Geometrical Restraints of His Residues
A recent paper, already listed on this bulletin board, will give you a hint about improving the geometrical restraints of His residues, depending on their protonation/tautomeric form, especially at high resolution:

M.Malinska, M.Dauter, M.Kowiel, M.Jaskolski, Z.Dauter (2015) Protonation and geometry of histidine rings. Acta Cryst. D71, 1444-1454.

This may be a good occasion to mention that for years Refmac has been using the older (1991) version (containing errors) of the Engh & Huber stereochemical dictionary, even though the authors themselves (E&H) corrected it in 2001...

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)