Biological Crystallography

 

Acta Cryst. (2005). D61, 1173-1180  [ doi:10.1107/S0907444905019451 ]

Post-crystallization treatments for improving diffraction quality of protein crystals

B. Heras and J. L. Martin

Synopsis: This review provides a compilation of post-crystallization methods that can convert poorly diffracting crystals into data-quality crystals. Protocols for annealing, dehydration, soaking and cross-linking are outlined and examples of some spectacular changes in crystal quality are provided.

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1181-1189  [ doi:10.1107/S090744490501543X ]

Regular arrangement of periodates bound to lysozyme

J. Ondrácek, M. S. Weiss, J. Brynda, J. Fiala, F. Jursík, P. Rezácová, L. B. Jenner and J. Sedlácek

Synopsis: The structure of the periodate complex of lysozyme has been determined, refined and analyzed.

PDB reference: 1hc0

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1190-1198  [ doi:10.1107/S0907444905017488 ]

Structures of the oxidized and reduced forms of nitrite reductase from Rhodobacter sphaeroides 2.4.3 at high pH: changes in the interactions of the type 2 copper

F. Jacobson, H. Guo, K. Olesen, M. Ökvist, R. Neutze and L. Sjölin

Synopsis: The crystal structures of oxidised and reduced nitrite reductase from R. sphaeroides give new insight into the pH dependence of nitrite binding to the active site.

PDB references: 1zv2 and 2a3t

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1199-1206  [ doi:10.1107/S0907444905017531 ]

Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms

J. M. Johnston, V. L. Arcus and E. N. Baker

Synopsis: The crystal structures of naphthoate synthase (MenB) and its complex with the product naphthoyl-CoA have been determined by X-ray crystallography at resolutions of 2.15 and 2.30 Å, respectively. The native structure shows several flexible regions around the active site which are only partly rigidified by the bound ligand.

PDB references: 1rjm and 1rjn

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1207-1212  [ doi:10.1107/S0907444905017841 ]

Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii

P. H. Rehse and T. H. Tahirov

Synopsis: The crystal structure of a putative 2'-5' RNA ligase from P. horikoshii was solved and compared with a Thermus thermophilus homologue and the structurally related cyclic phosphodiesterase.

PDB reference: 1vdx

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1213-1221  [ doi:10.1107/S0907444905018317 ]

Structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum

J. F. Satchell, R. L. Malby, C. S. Luo, A. Adisa, A. E. Alpyurek, N. Klonis, B. J. Smith, L. Tilley and P. M. Colman

Synopsis: The structure of P. falciparum GAPDH has been solved to 2.6 Å resolution with one molecule of NAD⁺ bound per subunit. Amino-acid substitutions which cluster in a groove about the R dyad suggest a potential binding site for haem, which is known to specifically inhibit the Plasmodium enzyme.

PDB reference: 1ywg

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1222-1226  [ doi:10.1107/S0907444905018834 ]

Structure of yeast 5-aminolaevulinic acid dehydratase complexed with the inhibitor 5-hydroxylaevulinic acid

P. T. Erskine, L. Coates, R. Newbold, A. A. Brindley, F. Stauffer, G. D. E. Beaven, R. Gill, A. Coker, S. P. Wood, M. J. Warren, P. M. Shoolingin-Jordan, R. Neier and J. B. Cooper

Synopsis: The X-ray structure of the enzyme 5-aminolaevulinic acid dehydratase (ALAD) from yeast complexed with the competitive inhibitor 5-hydroxylaevulinic acid has been determined at a resolution of 1.9 Å.

PDB reference: 1w31

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1227-1237  [ doi:10.1107/S0907444905019360 ]

Improving radiation-damage substructures for RIP

M. H. Nanao, G. M. Sheldrick and R. B. G. Ravelli

Synopsis: A simple method for treating RIP data is presented which improves the quality of RIP substructures as well as the phases from downstream phasing applications.

PDB references: 2blo, 2blq, 2bn3, 2bn1, 2blx, 2bly, 2blp, 2blz, 2blr, 2blu, 2blv and 2blw

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1238-1244  [ doi:10.1107/S0907444905019761 ]

Overcoming the false-minima problem in direct methods: structure determination of the packaging enzyme P4 from bacteriophage 13

C. Meier, E. J. Mancini, D. H. Bamford, M. A. Walsh, D. I. Stuart and J. M. Grimes

Synopsis: The problems encountered during the phasing and structure determination of the packaging enzyme P4 from bacteriophage 13 which arise from the arrangement of the four hexamers comprising the crystallographic asymmetric unit are described.

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1245-1254  [ doi:10.1107/S0907444905020251 ]

Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine

C. Schnick, M. A. Robien, A. M. Brzozowski, E. J. Dodson, G. N. Murshudov, L. Anderson, J. R. Luft, C. Mehlin, W. G. J. Hol, J. A. Brannigan and A. J. Wilkinson

Synopsis: The malarial purine nucleoside phosphorylase (PNP) in complexes with inosine and with sulfate, are reported. These structures are compared with a previous structure of P. falciparum PNP in complex with a transition-state inhibitor.

PDB references: 2bsx and 1sq6

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1255-1262  [ doi:10.1107/S0907444905021207 ]

Structure of Ecballium elaterium trypsin inhibitor II (EETI-II): a rigid molecular scaffold

R. Krätzner, J. É. Debreczeni, T. Pape, T. R. Schneider, A. Wentzel, H. Kolmar, G. M. Sheldrick and I. Uson

Synopsis: The cystine-knot protein EETI-II is shown to be particularly rigid.

PDB references: 1w7z, 1h9h and 1h9i

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1263-1272  [ doi:10.1107/S0907444905021475 ]

On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength

C. Mueller-Dieckmann, S. Panjikar, P. A. Tucker and M. S. Weiss

Synopsis: Based on the evaluation of a large number of experiments carried out at different X-ray wavelengths with respect to the anomalous signal-to-noise ratio, the optimum wavelength for diffraction data collection was found to be close to 2.1 Å irrespective of the nature of the anomalously scattering substructure.

PDB references: 2a7a, 2a7b, 2a7c, 2a7d, 2a7e, 2a7f, 2a7g, 2a7h, 2a7i and 2a7j

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1273-1279  [ doi:10.1107/S0907444905021487 ]

Structures of aminoglycoside acetyltransferase AAC(6')-Ii in a novel crystal form: structural and normal-mode analyses

D. L. Burk, B. Xiong, C. Breitbach and A. M. Berghuis

Synopsis: The structure of the antibiotic resistance factor AAC(6')-Ii in complex with coenzyme A has been determined in a new crystal form. Comparison of this structure with the previously determined complex and in combination with normal-mode analysis reveals conformational plasticity that may be important to enzymatic mechanism.

PDB reference: 2a4n

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1280-1288  [ doi:10.1107/S0907444905021566 ]

Protein crystallization in hydrogel beads

R. Willaert, I. Zegers, L. Wyns and M. Sleutel

Synopsis: The use of hydrogel beads for the crystallization of proteins is explored in this contribution.

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1289-1298  [ doi:10.1107/S0907444905022316 ]

Radiation-induced site-specific damage of mercury derivatives: phasing and implications

U. A. Ramagopal, Z. Dauter, R. Thirumuruhan, E. Fedorov and S. C. Almo

Synopsis: Analysis of data collected from Hg-derivatized crystals reveals that mercury-cysteine bonds are very susceptible to radiation damage.

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1299-1301  [ doi:10.1107/S0907444905019591 ]

Bulk-solvent correction in large macromolecular structures

B. Rees, L. Jenner and M. Yusupov

Synopsis: It is shown that the standard bulk-solvent corrrection, as implemented in CNS, can lead to incorrect results in the case of large macromolecular structures. A modified method of the solvent mask definition is proposed.

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1302-1305  [ doi:10.1107/S0907444905019670 ]

Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions

M. Sugahara, Y. Asada, H. Ayama, H. Ukawa, H. Taka and N. Kunishima

Synopsis: Heavy-atom Database System is a program that assists heavy-atom derivatization of proteins. On the basis of amino-acid sequence/motif and crystallization conditions, the program suggests potential heavy-atom reagents for any target protein by searching against a database of known heavy-atom derivatives.

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1306-1310  [ doi:10.1107/S0907444905018822 ]

Surface-entropy reduction used in the crystallization of human choline acetyltransferase

A.-R. Kim, T. Dobransky, R. J. Rylett and B. H. Shilton

Synopsis: Surface-entropy reduction was used to obtain high-quality crystals of human choline acetyltransferase.

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1311  [ doi:10.1107/S0907444905024996 ]

Parameter-space screening: a powerful tool for high-throughput crystal structure determination. Corrigendum

Z.-J. Liu, D. Lin, W. Tempel, J. L. Praissman, J. P. Rose and B.-C. Wang

Synopsis: A corrigendum to the paper by Liu et al. (2005), Acta Cryst. D61, 520-527.

Online 16 August 2005

 

Acta Cryst. (2005). D61, 1312  [ doi:10.1107/S0907444905019621 ]

Unravelling the structural chemistry of the colouration mechanism in lobster shell. Erratum

N. E. Chayen, M. Cianci, J. G. Grossmann, J. Habash, J. R. Helliwell, G. A. Nneji, J. Raftery, P. J. Rizkallah and P. F. Zagalsky

Synopsis: An erratum to the paper by Chayen et al. (2003), Acta Cryst. D59, 2072-2082.

Online 16 August 2005