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Newsletter No. 356
June 19, 2017

ACA News, IUCr Newsletter, IUCr Meetings List

MAY 2017 PUBLICATIONS BY MEMBERS OF THE GROUP  

1: Trachman RJ 3rd, Demeshkina NA, Lau MWL, Panchapakesan SSS, Jeng SCY, Unrau
PJ, Ferré-D'Amaré AR. Structural basis for high-affinity fluorophore binding and
activation by RNA Mango
. Nat Chem Biol. 2017 May 29. doi: 10.1038/nchembio.2392.
[Epub ahead of print] PubMed PMID: 28553947.

2: Sheng Z, Schramm CA, Kong R; NISC Comparative Sequencing Program., Mullikin
JC, Mascola JR,
Kwong PD, Shapiro L. Gene-Specific Substitution Profiles Describe
the Types and Frequencies of Amino Acid Changes during Antibody Somatic
Hypermutation
. Front Immunol. 2017 May 10;8:537. doi: 10.3389/fimmu.2017.00537.
eCollection 2017. PubMed PMID: 28539926; PubMed Central PMCID: PMC5424261.

3: Liang B, Ngwuta JO, Surman S, Kabatova B, Liu X, Lingemann M, Liu X, Yang L,
Herbert R, Swerczek J, Chen M, Moin SM, Kumar A, McLellan JS,
Kwong PD, Graham
BS, Collins PL, Munir S. Improved prefusion stability, optimized codon-usage, and
augmented virion packaging enhance the immunogenicity of respiratory syncytial
virus (RSV) fusion protein in a vectored vaccine candidate
. J Virol. 2017 May 24.
pii: JVI.00189-17. doi: 10.1128/JVI.00189-17. [Epub ahead of print] PubMed PMID:
28539444.

4: Pyra A, Brzozowska E, Pawlik K, Gamian A, Dauter M,
Dauter Z. Tail tubular
protein A: a dual-function tail protein of Klebsiella pneumoniae bacteriophage
KP32
. Sci Rep. 2017 May 22;7(1):2223. doi: 10.1038/s41598-017-02451-3. PubMed
PMID: 28533535; PubMed Central PMCID: PMC5440376.

5: Ceccon A, Tugarinov V, Boughton AJ, Fushman D, Clore GM. Probing the Binding
Modes of a Multidomain Protein to Lipid-based Nanoparticles by Relaxation-based
NMR
. J Phys Chem Lett. 2017 Jun 1;8(11):2535-2540. doi:
10.1021/acs.jpclett.7b01019. Epub 2017 May 24. PubMed PMID: 28530812.

6: Cale EM, Gorman J, Radakovich NA, Crooks ET, Osawa K, Tong T, Li J, Nagarajan
R, Ozorowski G, Ambrozak DR, Asokan M, Bailer RT, Bennici AK, Chen X, Doria-Rose
NA, Druz A, Feng Y, Joyce MG, Louder MK, O'Dell S, Oliver C, Pancera M, Connors
M, Hope TJ, Kepler TB, Wyatt RT, Ward AB, Georgiev IS,
Kwong PD, Mascola JR,
Binley JM. Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing
Antibody that Lacks a Protruding Loop
. Immunity. 2017 May 16;46(5):777-791.e10.
doi: 10.1016/j.immuni.2017.04.011. PubMed PMID: 28514685.

7: Tomczak A, Singh K, Gittis AG, Lee J, Garboczi DN, Murphy PM. Biochemical and
biophysical characterization of cytokine-like protein 1 (CYTL1)
. Cytokine. 2017
May 4;96:238-246. doi: 10.1016/j.cyto.2017.04.023. [Epub ahead of print] PubMed
PMID: 28478073.

8: Pancera M, Changela A,
Kwong PD. How HIV-1 entry mechanism and broadly
neutralizing antibodies guide structure-based vaccine design
. Curr Opin HIV AIDS.
2017 May;12(3):229-240. doi: 10.1097/COH.0000000000000360. PubMed PMID: 28422787.

9: Jones CP, Ferré-D'Amaré AR. Long-Range Interactions in Riboswitch Control of
Gene Expression
. Annu Rev Biophys. 2017 May 22;46:455-481. doi:
10.1146/annurev-biophys-070816-034042. Epub 2017 Mar 30. PubMed PMID: 28375729.


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.

Mariusz Jaskolski
: Stereochemical Restraint Libraries for Nucleic Acids

As part of a project aimed at revising the stereochemical restraint libraries for nucleic acids, a server, RestraintLib, has been created. It prepares external (custom) restraint files for the phosphate groups in DNA and RNA structures (submitted as PDB files). At present, the output is prepared for Refmac5, but other formats will be added as well.

The discussion of the new restraints and the method of their generation are presented in Nucleic Acids Research Advanced Access published August 12, 2016.


Zbigniew Dauter (NCI): Data Completeness from HKL2000 or HKL3000

Sometimes, relatively weak diffraction data processed with HKL2000 or HKL3000 show lower than expected completeness in the high resolution bins, in spite of otherwise high multiplicity and coverage of the reciprocal space. Apparently, this results from the automatic rejection of weak reflections, for which there are no good enough neighbors for building a “standard profile” within the vicinity defined by default value of the “Profile Fitting Radius”. To increase the high-resolution data completeness one can change the default profile fitting radius (in the “Index” window of HKL2000 or HKL3000) to much larger value, e.g. one third of the detector size. The number of “good” reflections, e.g. stronger than 5s(I), within the profile fitting radius can be visualized at the Xdisp window by clicking the “Prof Fit R” option.

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, Structural Genomics, NCS, Missing Atoms, Trends in CrystallographyAbsorption Correction, Data for Refinement and Publication.

LECTURES AND TUTORIALS - PROTEIN CRYSTALLOGRAPHY
                                                         Methods and Protocols



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)

LITERATURE ON CRYSTALLOGRAPHY THEORY AND METHODS (2017)

PROTEIN CRYSTALLOGRAPHY Methods and Protocols (2017)

 LINKS - New Server: RestraintLib
  

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,
 
            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)