Biological Crystallography

 

Acta Cryst. (2005). D61, 1437-1448  [ doi:10.1107/S0907444905023589 ]

Anomalous signal indicators in protein crystallography

P. H. Zwart

Synopsis: Various anomalous signal indicators and their use in the last 50 years are reviewed. A Monte Carlo procedure is described that allows the estimation of a number of these indicators as well as the resulting cosine of the phase error as obtained from experimental SAD phases and the number of significant Bijvoet differences in a SAD data set.

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1449-1458  [ doi:10.1107/S0907444905025503 ]

Novel multisubstrate inhibitors of mammalian purine nucleoside phosphorylase

A. V. Toms, W. Wang, Y. Li, B. Ganem and S. E. Ealick

Synopsis: Development of novel multisubstrate inhibitors of bovine purine nucleoside phosphorylase is discussed.

PDB references: 2ai1, 2ai2 and 2ai3

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1459-1464  [ doi:10.1107/S0907444905025667 ]

Structure of inorganic pyrophosphatase from Helicobacter pylori

C. A. Wu, N. K. Lokanath, D. Y. Kim, H. J. Park, H.-Y. Hwang, S. T. Kim, S. W. Suh and K. K. Kim

Synopsis: The crystal structure of inorganic pyrophosphatase from H. pylori was determined at 2.6  Å resolution, revealing that structural flexibility of the loops near the active site is required for catalytic efficiency.

PDB reference: 1ygz

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1465-1475  [ doi:10.1107/S090744490502576X ]

A modified ACORN to solve protein structures at resolutions of 1.7  Å or better

Y. Jia-xing, M. M. Woolfson, K. S. Wilson and E. J. Dodson

Synopsis: The ACORN program has been extended to work with data to resolution down to 1.7  Å.

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1476-1482  [ doi:10.1107/S0907444905025771 ]

The structure of T₆ bovine insulin

G. D. Smith, W. A. Pangborn and R. H. Blessing

Synopsis: Although the structure of T₆ bovine insulin is nearly identical to that of porcine insulin, the loss of C¹ from isoleucine at residue A10 in porcine insulin to produce valine in bovine insulin results in a more efficient packing of the hexamers along the c axis.

PDB reference: 2a3g

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1483-1491  [ doi:10.1107/S0907444905026132 ]

Galactose recognition by the carbohydrate-binding module of a bacterial sialidase

S. L. Newstead, J. N. Watson, A. J. Bennet and G. Taylor

Synopsis: By studying nine crystallographically independent structures of M. viridifaciens sialidase, the relative flexibility of its three domains has been analysed. A detailed study is also presented of the recognition of galactose and lactose by the M. viridifaciens carbohydrate-binding module.

PDB reference: 2bq9

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1492-1499  [ doi:10.1107/S0907444905026673 ]

Structures of Mycobacterium tuberculosis pyridoxine 5'-phosphate oxidase and its complexes with flavin mononucleotide and pyridoxal 5'-phosphate

B. K. Biswal, M. M. Cherney, M. Wang, C. Garen and M. N. G. James

Synopsis: The X-ray structure of a conserved hypothetical protein of molecular weight 16.3  kDa from M. tuberculosis corresponding to the open reading frame Rv1155 has been solved and refined at 1.8  Å resolution. The structures of flavin mononucleotide (FMN) and pyridoxal 5'-phosphate (PLP) bound separately to Rv1155 have been determined at 2.2 and 1.7  Å resolution, respectively.

PDB references: 1xxo, 1y30 and 2aq6

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1500-1507  [ doi:10.1107/S090744490502651X ]

Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability

M. Sugahara, N. Ohshima, Y. Ukita, M. Sugahara and N. Kunishima

Synopsis: The structure of ATP-dependent phosphoenolpyruvate carboxykinase from T. thermophilus HB8 has been determined at 2.0  Å resolution. This first three-dimensional structure of a thermostable orthologue exhibits the so-called `conformational selection' mechanism of induced fit upon ATP binding. The polypeptide fold contains a bound calcium ion which has been suggested to be important for the thermostability of this enzyme.

PDB references: 1j3b and 1xkv

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1508-1513  [ doi:10.1107/S0907444905026740 ]

Structural analysis of human liver glyceraldehyde-3-phosphate dehydrogenase

S. A. Ismail and H. W. Park

Synopsis: The crystal structure of human liver glyceraldehyde-3-phosphate dehydrogenase is reported.

PDB reference: 1znq

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1514-1520  [ doi:10.1107/S0907444905027332 ]

FINDMOL: automated identification of macromolecules in electron-density maps

E. W. McKee, L. D. Kanbi, K. L. Childs, R. W. Grosse-Kunstleve, P. D. Adams, J. C. Sacchettini and T. R. Ioerger

Synopsis: The FINDMOL algorithm is designed to quickly locate contiguous symmetrically unique macromolecular regions from medium- to low-resolution skeletonized electron-density maps. It uses cluster analysis of trace points representing high-density regions. Higher level prior information such as sequence information is not required. In most cases, the resulting arrangement of trace points resembles the contiguous protein macromolecule.

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1521-1527  [ doi:10.1107/S0907444905027423 ]

Experimental methods for measuring accurate high-amplitude phases and their importance in isomorphous replacement experiments

A. S. Soares and Y. Vekhter

Synopsis: A limited number of accurate phases were measured for strong low resolution rhombohedral insulin reflections. These phases greatly improved initial map quality and subsequent density modification.

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1528-1532  [ doi:10.1107/S0907444905028003 ]

Crystal growth in X-ray-transparent plastic tubing: an alternative for high-throughput applications

Y. Kalinin and R. Thorne

Synopsis: A simple method for growing protein crystals in thin-wall water-permeable plastic tubing provides greater kinetic control and simplifies setup, handling and crystal retrieval. Tubing thicknesses that give desirable permeability and mechanical properties produce little X-ray scatter and allow rapid in situ flash-cooling.

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1533-1540  [ doi:10.1107/S0907444905028416 ]

Comparison of phasing methods for sulfur-SAD using in-house chromium radiation: case studies for standard proteins and a 69  kDa protein

N. Watanabe, Y. Kitago, I. Tanaka, J. Wang, Y. Gu, C. Zheng and H. Fan

Synopsis: Three phasing methods were compared for data sets collected with a Cr  K X-ray source using loopless data collection. Phasing with OASIS-2004 gave the best results for four standard proteins and the 69  kDa protein TT0570.

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1541-1549  [ doi:10.1107/S0907444905028532 ]

A comparison of refined X-ray structures of hydrogenated and perdeuterated rat E-crystallin in H₂O and D₂O

J.-B. Artero, M. Härtlein, S. McSweeney and P. Timmins

Synopsis: Comparison between hydrogenated and deuterated E-crystallin crystals in H₂O and in D₂O solvent.

PDB references: 1zgt, 1zie, 1zir and 1ziq

Online 19 October 2005

 

Acta Cryst. (2005). D61, 1550-1562  [ doi:10.1107/S0907444905028805 ]

Structure of human semicarbazide-sensitive amine oxidase/vascular adhesion protein-1

E. Jakobsson, J. Nilsson, D. Ogg and G. J. Kleywegt

Synopsis: The crystal structure of a truncated, soluble form of human semicarbazide-sensitive amine oxidase, also know as vascular adhesion protein-1, is described.

PDB references: 2c10 and 2c11

Online 19 October 2005