Biological Crystallography

 

Acta Cryst. (2007). D63, 1029-1041  [ doi:10.1107/S0907444907038164 ]

Structure-factor extrapolation using the scalar approximation: theory, applications and limitations

U. K. Genick

Synopsis: The scalar approximation to structure-factor extrapolation (SASFE) procedure is used to extrapolate structure-factor amplitudes for a fully `activated' crystal from amplitudes of a native and a partially activated crystal. Here, it is investigated whether and under what conditions the approximations inherent in SASFE introduce significant errors. The results indicate that the errors introduced by SASFE's assumptions are negligible and that SASFE's usefulness in macromolecular crystallography is limited primarily by the propagation of experimental uncertainties.

Online 19 September 2007

 

Acta Cryst. (2007). D63, 1042-1047  [ doi:10.1107/S0907444907038292 ]

Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons

Y. Sato, Y. Maeda, S. Shimizu, M. T. Hossain, S. Ubukata, K. Suzuki, T. Sekiguchi and A. Takénaka

Synopsis: The crystal structure of St-AspRS (nondiscriminating type) has been determined at 2.3 Å resolution as the first example of the nondiscriminating type of AspRS from crenarchaea.

PDB reference: 1wyd

Online 19 September 2007

 

Acta Cryst. (2007). D63, 1048-1058  [ doi:10.1107/S090744490703836X ]

Structure of an aliphatic amidase from Geobacillus pallidus RAPc8

S. W. Kimani, V. B. Agarkar, D. A. Cowan, M.F.-R. Sayed and B. T. Sewell

Synopsis: The homohexameric structure of a member of the nitrilase superfamily with D3 symmetry. The active site configuration suggests a catalytic role for Glu142.

PDB reference: 2plq

Online 19 September 2007

 

Acta Cryst. (2007). D63, 1059-1068  [ doi:10.1107/S0907444907040668 ]

Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis

S. Goto-Ito, R. Ishii, T. Ito, R. Shibata, E. Fusatomi, S. Sekine, Y. Bessho and S. Yokoyama

Synopsis: The crystal structure of P. horikoshii TYW1 is described.

PDB reference: 2yx0

Online 19 September 2007

 

Acta Cryst. (2007). D63, 1069-1074  [ doi:10.1107/S0907444907042230 ]

Structure determination of the O-methyltransferase NovP using the `free lunch algorithm' as implemented in SHELXE

I. Usón, C. E. M. Stevenson, D. M. Lawson and G. M. Sheldrick

Synopsis: The crystal structure of NovP, an O-methyltransferase comprising 262 amino acids, was solved by SIRAS using 1.35 Å native data and 2.45 Å data from a single mercury derivative using a combination of partial chain tracing by hand of the initial very noisy map followed by data extrapolation to 1.0 Å resolution.

Online 19 September 2007

 

Acta Cryst. (2007). D63, 1075-1081  [ doi:10.1107/S0907444907042229 ]

Conformational switches in winged-helix domains 1 and 2 of bacterial translation elongation factor SelB

O. Ganichkin and M. C. Wahl

Synopsis: The first two winged-helix motifs of domain IV of translation elongation factor SelB from M. thermoacetica can undergo conformational switches, which could support a functional interaction between the N- and C-terminal portions of SelB.

PDB reference: 2v9v

Online 19 September 2007

 

Acta Cryst. (2007). D63, 1082-1093  [ doi:10.1107/S0907444907042461 ]

Refined crystal structures of red and green fluorescent proteins from the button polyp Zoanthus

N. Pletneva, V. Pletnev, T. Tikhonova, A. A. Pakhomov, V. Popov, V. I. Martynov, A. Wlodawer, Z. Dauter and S. Pletnev

Synopsis: The crystal structure of the red fluorescent protein zRFP574 from Zoanthus sp. 2 at 1.51 Å resolution allowed a detailed description of the chromophore derived from decarboxylation of the aspartate side chain within the chromophore-forming tripeptide Asp-Tyr-Gly. Comparison with the newly determined X-ray structure of the green fluorescent protein zGFP506 from a related Zoanthus species and its mutant zGFP506_N66D in the transitional `green' and mature `red' forms provides new insight into the structural chemistry responsible for the acquisition of red fluorescence.

PDB references: 2icr, 2ojk, 2pxw and 2pxs

Online 19 September 2007

 

Acta Cryst. (2007). D63, 1094-1101  [ doi:10.1107/S0907444907043417 ]

X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata

V. de Serrano, Z. Chen, M. F. Davis and S. Franzen

Synopsis: In order to investigate the dual function of the dehaloperoxidase from the terebellid polychaete Amphitrite ornata, the enzyme was expressed in Escherichia coli as a recombinant protein in its wild-type form and as a mutant protein. Both the wild-type and mutant proteins were crystallized and their structures were determined at 100 K to a resolution of 1.62 Å.

PDB references: 2qfk and 2qfn

Online 19 September 2007

 

Acta Cryst. (2007). D63, 1102-1108  [ doi:10.1107/S0907444907043363 ]

Structure of sylvaticin, a new -elicitin-like protein from Pythium sylvaticum

M.-B. Lascombe, P. Retailleau, M. Ponchet, B. Industri, J.-P. Blein and T. Prangé

Synopsis: Sylvaticin, a 10 kDa protein excreted by the Oomycete Pythium sylvaticum reveals an -elicitin-like structure with a reduced internal cavity.

PDB references: 2pos and 2pr0

Online 19 September 2007

 

Acta Cryst. (2007). D63, 1109-1112  [ doi:10.1107/S090744490704228X ]

Structure of the RuBisCO chaperone RbcX from Synechocystis sp. PCC6803

S. Tanaka, M. R. Sawaya, C. A. Kerfeld and T. O. Yeates

Synopsis: The crystal structure of RbcX from Synechocystis sp. PCC6803 is reported, revealing an unusually long protruding C-terminal helix, as well as a bound polyethylene glycol molecule in the protein substrate-binding site.

PDB reference: 2py8

Online 19 September 2007

 

Acta Cryst. (2007). D63, 1113-1114  [ doi:10.1107/S0907444907041406 ]

Comment on Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? by Jaskolski, Gilski, Dauter & Wlodawer (2007)

B. Stec

Synopsis: Comment on Jaskolski et al. [(2007), Acta Cryst. D63, 611-620].

Online 19 September 2007