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Newsletter No. 360
September 4, 2017

ACA News, IUCr Newsletter, IUCr Meetings List

AUGUST 2017 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Mayer ML. The Challenge of Interpreting Glutamate-Receptor Ion-Channel
Structures
. Biophys J. 2017 Aug 24. pii: S0006-3495(17)30854-8. doi:
10.1016/j.bpj.2017.07.028. [Epub ahead of print] Review. PubMed PMID: 28844473.

2: Spencer M, Max N, Ireland J, Zou Z, Wang R,
Sun PD. Over-expression of a human
CD62L ecto-domain and a potential role of RNA pseudoknot structures in
recombinant protein expression
. Protein Expr Purif. 2017 Aug 24;140:65-73. doi:
10.1016/j.pep.2017.08.008. [Epub ahead of print] PubMed PMID: 28842197.

3: Liu X, Liang B, Ngwuta J, Liu X, Surman S, Lingemann M,
Kwong PD, Graham BS,
Collins PL, Munir S. Attenuated human parainfluenza virus type 1 (HPIV1)
expressing the respiratory syncytial virus (RSV) fusion F glycoprotein from an
added gene: effects of pre-fusion stabilization and packaging of RSV F
. J Virol.
2017 Aug 23. pii: JVI.01101-17. doi: 10.1128/JVI.01101-17. [Epub ahead of print]
PubMed PMID: 28835504.

4: Pancera M, Lai YT, Bylund T, Druz A, Narpala S, O'Dell S, Schön A, Bailer RT,
Chuang GY, Geng H, Louder MK, Rawi R, Soumana DI, Finzi A, Herschhorn A, Madani
N, Sodroski J, Freire E, Langley DR, Mascola JR, McDermott AB,
Kwong PD. Crystal
structures of trimeric HIV envelope with entry inhibitors BMS-378806 and
BMS-626529
. Nat Chem Biol. 2017 Aug 21. doi: 10.1038/nchembio.2460. [Epub ahead
of print] PubMed PMID: 28825711.

5: O'Carroll IP, Thappeta Y, Fan L, Ramirez-Valdez EA, Smith S, Wang YX, Rein A.
Contributions of individual domains to function of the HIV-1 Rev response
element
. J Virol. 2017 Aug 16. pii: JVI.00746-17. doi: 10.1128/JVI.00746-17.
[Epub ahead of print] PubMed PMID: 28814520.

6: Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K,
Kunkel TA, Wilson SH. Time-lapse crystallography snapshots of a double-strand
break repair polymerase in action
. Nat Commun. 2017 Aug 15;8(1):253. doi:
10.1038/s41467-017-00271-7. PubMed PMID: 28811466; PubMed Central PMCID:
PMC5557891.

7: Wälti MA, Schmidt T, Murray DT, Wang H, Hinshaw JE, Clore GM. Chaperonin GroEL
accelerates protofibril formation and decorates fibrils of the Het-s prion
protein
. Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):9104-9109. doi:
10.1073/pnas.1711645114. Epub 2017 Aug 7. PubMed PMID: 28784759.

8: Schwieters CD, Bermejo GA,
Clore GM. Xplor-NIH for Molecular Structure
Determination from NMR and Other Data Sources
. Protein Sci. 2017 Aug 2. doi:
10.1002/pro.3248. [Epub ahead of print] PubMed PMID: 28766807.

9: Botos I, Noinaj N, Buchanan SK. Insertion of proteins and lipopolysaccharide
into the bacterial outer membrane
. Philos Trans R Soc Lond B Biol Sci. 2017 Aug
5;372(1726). pii: 20160224. doi: 10.1098/rstb.2016.0224. Review. PubMed PMID:
28630161; PubMed Central PMCID: PMC5483524.

For timely listing, please send a heads-up E-mail to the Editor upon publication.
TIPS, TRICKS, METHODS - A Convenient Phasing Vehicle

Zbigniew Dauter (NCI): Selenourea: A Convenient Phasing Vehicle

Majority of novel X-ray crystal structures of proteins are currently solved using the anomalous diffraction signal provided by selenium after incorporation of selenomethionine instead of natural methionine by genetic engineering methods. However, selenium can be also inserted into protein crystals in the form of selenourea (SeC(NH2)2), by adding selenourea into mother liquor or cryo-solution or in the form of powder into a drop with native crystals, in analogy to the classic procedure of heavy-atom derivatization. Selenourea is able to bind to reactive groups at the surface of macromolecules primarily through hydrogen bonds, where the selenium atom may serve as acceptor and amide groups as H-bond donors. Selenourea has different chemical properties than other heavy-atom reagents and halide ions and provides a convenient way of phasing crystal structures of macromolecules. A de novo protein crystal structure at low resolution of 2.9 Å with total 1125 residues distributed in seven chains in asymmetric unit at was recently successfully solved with this method. For details, see Selenourea: a convenient phasing vehicle for macromolecular X-ray crystal structures, Sci. Rep. 6, 37123 (2016) by Zhipu Luo.


Xinhua Ji
: It was recently reported that microseeding was used to produce untwinned crystals of an O-demethylase using twinned crystals as seeds (Acta Crystal. F72:897-902, 2016). Microseeding separates nucleation events from crystal growth events so that it can yield different crystal forms. Hence, it is promising that this technique can be used to produce untwinned crystals from twinned seeds.

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

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.

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 Publication.

LECTURES AND TUTORIALS 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 - New Server: RestraintLib
  

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 (http://mcl1.ncifcrf.gov)