Biological Crystallography

 

Acta Cryst. (2007). D63, 555-563  [ doi:10.1107/S0907444907005616 ]

Structure of the mexicain-E-64 complex and comparison with other cysteine proteases of the papain family

J. A. Gavira, L. A. González-Ramírez, M. C. Oliver-Salvador, M. Soriano-García and J. M. García-Ruiz

Synopsis: A comparison of the binding site of mexicain for E-64 with those of other E-64-cysteine protease complexes shows that highly conserved interactions are replaced by other interactions in which water molecules play an essential role.

PDB reference: 2bdz

Online 21 April 2007

 

Acta Cryst. (2007). D63, 564-570  [ doi:10.1107/S0907444907007810 ]

Heterogeneous nucleation of three-dimensional protein nanocrystals

D. G. Georgieva, M. E. Kuil, T. H. Oosterkamp, H. W. Zandbergen and J. P. Abrahams

Synopsis: Human hair was identified to be a versatile nucleant surface and was applied successfully for the crystallization of various proteins. Despite the rather complex mechanism of heterogeneous crystallization, it was discovered that the surface properties and the chemical composition together define the nucleation properties of the selected surface.

Online 21 April 2007

 

Acta Cryst. (2007). D63, 571-580  [ doi:10.1107/S0907444907007871 ]

Structures of vaccinia virus dUTPase and its nucleotide complexes

A. Samal, N. Schormann, W. J. Cook, L. J. DeLucas and D. Chattopadhyay

Synopsis: The vaccinia virus dUTPase structure shows an increased size of the central channel within the homotrimer.

PDB references: 2okb, 2okd, 2oke, 2ol0 and 2ol1

Online 21 April 2007

 

Acta Cryst. (2007). D63, 581-586  [ doi:10.1107/S0907444907008372 ]

Structure of the equine arteritis virus nucleocapsid protein reveals a dimer-dimer arrangement

A. Deshpande, S. Wang, M. A. Walsh and T. Dokland

Synopsis: Arteriviruses form a family of enveloped, positive-sense RNA viruses that includes important agricultural pathogens such as EAV. The EAV nucleocapsid protein forms an arrangement of dimers in the crystal structure that may reflect its organization in the virus.

PDB reference: 2i9f

Online 21 April 2007

 

Acta Cryst. (2007). D63, 587-596  [ doi:10.1107/S0907444907009110 ]

Structure of a CBS-domain pair from the regulatory 1 subunit of human AMPK in complex with AMP and ZMP

P. Day, A. Sharff, L. Parra, A. Cleasby, M. Williams, S. Hörer, H. Nar, N. Redemann, I. Tickle and J. Yon

Synopsis: The structure of a CBS-domain pair from human AMPK 1 in complex with the physiological activator AMP and the pharmacological activator ZMP (AICAR) is presented.

PDB references: 2uv4, 2uv5, 2uv6 and 2uv7

Online 21 April 2007

 

Acta Cryst. (2007). D63, 597-610  [ doi:10.1107/S0907444907009791 ]

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, P. D. Adams, N. W. Moriarty, P. Zwart, R. J. Read, D. Turk and L.-W. Hung

Synopsis: Heterogeneity in ensembles generated by independent model rebuilding principally reflects the limitations of the data and of the model-building process rather than the diversity of structures in the crystal.

Online 21 April 2007

    

Acta Cryst. (2007). D63, 611-620  [ doi:10.1107/S090744490700978X ]

Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?

M. Jaskolski, M. Gilski, Z. Dauter and A. Wlodawer

Synopsis: An evaluation of the geometrical restraints used in the refinement of protein structures is presented based on currently available protein and small-molecule structural databases.

Online 21 April 2007

 

Acta Cryst. (2007). D63, 621-627  [ doi:10.1107/S0907444907009961 ]

Probing the oxygen-binding site of the human formylglycine-generating enzyme using halide ions

D. Roeser, B. Schmidt, A. Preusser-Kunze and M. G. Rudolph

Synopsis: The human formylglycine-generating enzyme was cocrystallized with bromide and iodide ions, which, among other positions, occupy an oxygen-binding pocket that is crucial for enzyme catalysis. Halide ions may substitute for xenon in the detection of oxygen-binding sites.

PDB references: 2hi8 and 2hib

Online 21 April 2007

 

Acta Cryst. (2007). D63, 628-635  [ doi:10.1107/S0907444907010888 ]

A Rac1-GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium

G. Prehna and C. E. Stebbins

Synopsis: The crystal structure of a Rac1-GDP-Zn complex shows that Rac1 can coordinate zinc in a tetrahedral fashion by using residues in its biologically relevant switch I and switch II structural regions. Additionally, zinc can replace the normally coordinated magnesium without the perturbation of GDP from the small GTPase.

PDB reference: 2p2l

Online 21 April 2007

 

Acta Cryst. (2007). D63, 636-645  [ doi:10.1107/S0907444907010931 ]

Protein crystallization by surface entropy reduction: optimization of the SER strategy

D. R. Cooper, T. Boczek, K. Grelewska, M. Pinkowska, M. Sikorska, M. Zawadzki and Z. Derewenda

Synopsis: A systematic study of the effect of substituting five different residues for large, solvent-exposed and flexible amino acids has been conducted using traditional and alternate reservoir screens. The results suggest a strategy that may enhance the success rates of preparation of X-ray quality crystals of proteins that are otherwise recalcitrant to crystallization in their wild-type form.

PDB references: 2bxw, 2jhs, 2jht, 2jhu, 2jhv, 2jhw, 2jhx, 2jhy, 2jhz and 2ji0

Online 21 April 2007

 

Acta Cryst. (2007). D63, 646-652  [ doi:10.1107/S0907444907011109 ]

Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand

A. Cámara-Artigas, A. Palencia, J. C. Martínez, I. Luque, J. A. Gavira and J. M. García-Ruiz

Synopsis: The crystallographic structure of the N114A mutant of the SH3 domain of the Abelson leukaemia virus tyrosine kinase complexed with a high-affinity peptide is reported. An X-ray diffraction data set was collected directly from crystals from the initial screening using the capillary counter-diffusion technique.

PDB reference: 2o88

Online 21 April 2007

 

Acta Cryst. (2007). D63, 653-659  [ doi:10.1107/S0907444907011924 ]

High-pressure cryocooling for capillary sample cryoprotection and diffraction phasing at long wavelengths

C. U. Kim, Q. Hao and S. M. Gruner

Synopsis: It is shown that a high-pressure cryocooling method enables the phasing of macromolecular structures using either Xe or native S atoms. The method may even be used for crystals in capillaries.

PDB references: 2oqu and 2oqn

Online 21 April 2007

 

Acta Cryst. (2007). D63, 660-664  [ doi:10.1107/S0907444907015053 ]

Notes of a protein crystallographer: quo vadis structural biology?

C. Abad-Zapatero

Synopsis: The origins of molecular and structural biology are briefly discussed in the context of the current status of the field. The future of structure biology is reviewed suggesting that in order to reach a new level of understanding of biological processes is necessary to include the notions of dissipative structures within the conceptual framework of non-equilibrium thermodynamics.

Online 21 April 2007