Carl-Ivar Brändén (1934–2004)

Obituary for Carl-Ivar Brändén.

Structure of DsbC from Haemophilus influenzae

DsbC forms a flexible dimer that can accommodate a wide variety of protein substrates for disulfide-bond isomerization.

Ab initio phasing based on topological restraints: automated determination of the space group and the number of molecules in the unit cell

Dependence of ab initio connectivity-based phasing on its principal parameters allows an automated indication of the space group and of the number of molecules in the unit cell.

Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B

The crystal structure of apo protein tyrosine phosphatase 1B has been determined to 1.95 Å resolution. The structure shows four highly coordinated water molecules in the active site of the enzyme and the WPD-loop in a closed conformation.

Accurate automatic protein models

Main-chain molecular fragments are positioned in electron density by a phased rotation and translation function. The fragments are refined as flexible generalized atoms and connected into chains. The sequence is aligned and side chains are built. The overall accuracy of the protein model is about 0.2 Å at a resolution of 1.2–1.9 Å.

Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions

To demonstrate a new strategy for engineering crystal lattices through metal-mediated interactions, apo acyl carrier protein has been crystallized in the presence of zinc ions. The structure was solved with MAD phasing using zinc anomalous signals.

Ligand-binding and metal-exchange crystallographic studies on shrimp alkaline phosphatase

Shrimp alkaline phosphatase has been subjected to inhibitor and metal-exchange studies, which induced conformational changes in the active site.

Statistical experimental design of protein crystallization screening revisited

A statistical design approach is proposed to screen for and optimize protein crystallization conditions.

Structure of the cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni

The crystal structure of the first human parasite superoxide dismutase is described. Alternate positions for the catalytic copper are described along with differences within the electrostatic loops used for substrate guidance.

Observation of time-resolved structural changes by linear interpolation of highly redundant X-ray diffraction data

Linear interpolation of X-ray intensities from redundant data sets was used to determine the structures of insulin at different time points throughout the data collection. The structures reveal time-dependent structural changes that result from radiation exposure.

A redetermination of the structure of the triple mutant (K53,56,120M) of phospholipase A₂ at 1.6 Å resolution using sulfur-SAS at 1.54 Å wavelength

The crystal structure of the triple mutant (K53,56,120M) of a small protein (14 kDa), bovine pancreatic phospholipase A₂, has been redetermined using sulfur single-wavelength anomalous scattering (S-SAS) at 1.6 Å resolution using a wavelength of 1.54 Å.

Structure of the Yersinia pestis type III secretion chaperone SycH in complex with a stable fragment of YscM2

The structure of the type III secretion chaperone SycH from Y. pestis has been solved in complex with a stable fragment of YscM2, a negative regulator of type III secretion.

Structure of serine acetyltransferase from Haemophilus influenzae Rd

The structure of serine acetyltransferase from H. influenzae Rd determined at 2.7 Å resolution is presented. The structure is a hexamer consisting of a dimer of trimers, each of which contains subunits characterized by a conserved N-terminal α-helical domain and a C-terminal left-handed parallel β-helix.

Structural genomics of Caenorhabditis elegans: structure of the BAG domain

The crystal structure of BAG-1 protein from C. elegans reveals a new BAG-domain fold.

Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coli

Transcription factor DksA from E. coli, which contains a canonical Zn-finger motif, was cloned expressed, purified and crystallized. The crystals diffract beyond 2.0 Å resolution at a synchrotron and three complete multiple anomalous dispersion data sets were collected at the absorption edge of the Zn atom.

Cloning, expression, crystallization and initial crystallographic analysis of the C-terminal domain of the amyloid precursor protein APP

The C-terminal domain CAPPD of the β-amyloid precursor protein, a type I transmembrane protein involved in Alzheimer's disease, was cloned, expressed in E. coli and, after purification, also crystallized. The initial electron-density map was of good quality and showed mostly helical regions.

Expression, purification, crystallization and preliminary X-ray diffraction studies of the cmcI component of Streptomyces clavuligerus 7α-cephem-methoxylase

The expression, purification, crystallization and preliminary X-ray diffraction studies of the gene product of cmcI from S. clavuligerus is reported. CmcI is believed to control the conversion of cephalosporins to cephamycins via 7α-methoxylation.

Crystallization and preliminary X-ray analysis of carboxypeptidase Y inhibitor I^C complexed with the cognate proteinase

Carboxypeptidase Y inhibitor I^C, complexed with the cognate proteinase, was crystallized and X-ray diffraction data were collected to 2.7 Å resolution.

Crystallization of a non-B and a B mutant HIV protease

Two new HIV proteases isolated from Brazilian patients failing intensive anti-AIDS therapy, namely subtype B mutant and subtype F wild type protein, were crystallized. The crystallization procedure and the molecular replacement solution for both proteins are presented in this paper.

Purification, crystallization and preliminary crystallographic data of the m₃G cap-binding domain of human snRNP import factor snurportin 1

Full-length SPN1 did not crystallize, so fragments with m₃G cap binding activity were generated by protease cleavage. The crystals of a 26 kDa fragment which were obtained had to be enlarged by two rounds of microseeding.

Biochemical, biophysical and preliminary X-ray crystallographic analyses of the fusion core of Sendai virus F protein

The Sendai virus fusion-core six-helix bundle assembly was crystallized; crystals diffract X-rays to 2.5 Å resolution.

Crystallization and preliminary X-ray analyses of desulfurization enzyme DszB and its C27S mutant complexed with bi­phenyl-2-sulfinic acid

Crystallization and preliminary X-ray analyses of desulfurization enzyme DszB were conducted.

Crystallization and preliminary X-ray diffraction analysis of HeLp, a heme lipoprotein from the hemolymph of the cattle tick Boophilus microplus

The main protein from the hemolymph of the cattle tick B. microplus has been crystallized using 1,6-hexanediol. The crystals belonged to the triclinic space group P1 and diffracted up to 2.1 Å resolution.

Crystallization and preliminary X-ray analysis of Escherichia coli MutT in binary and ternary complex forms

E. coli MutT was crystallized in binary and ternary complex forms. The crystals diffracted to 1.96 and 2.56 Å resolution, respectively.

Crystallization and preliminary X-ray analysis of heparinase II from Pedobacter heparinus

The crystallization and preliminary X-ray analysis of heparinase II from P. heparinus is reported. Heparinases from P. heparinus are widely used in medical and analytical applications; however, their three-dimensional structures and detailed catalytic mechanisms have yet to be determined.

Purification, crystallization and preliminary X-ray analysis of Triatoma virus (TrV) from Triatoma infestans

Triatoma virus (TrV) is a viral pathogen of blood-sucking reduviid bugs (triatomines). This work describes the purification of TrV particles from infected T. infestans and their crystallization and preliminary crystallographic analyses.

Expression, purification and preliminary crystallographic studies of human coactosin-like protein

Human coactosin-like protein has been expressed in high yield and the His-tagged protein was purified by affinity chromatography. Several different crystal forms were obtained by the hanging-drop vapour-diffusion method.

Crystallization and preliminary crystallographic studies of the cofactor-binding domain of the LysR-type transcriptional regulator Cbl from Escherichia coli

The cofactor-binding domain of the LysR-type transcriptional regulator Cbl from E. coli has been cloned, overexpressed, purified and crystallized. The crystals diffract to 3.0 Å resolution using synchrotron radiation.

Crystallization of the xeroderma pigmentosum group F endonuclease from Aeropyrum pernix

Three different crystal forms of apXPF were grown in trigonal, monoclinic and triclinic systems. The trigonal crystals diffracted to 2.8 Å and were grown in the presence of double-stranded DNA. Monoclinic crystals were grown without DNA and diffracted to 3.2 Å. Triclinic crystals were grown from a truncated apXPF protein lacking the tandem helix–hairpin–helix motifs and diffracted to 2.1 Å.

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic investigations of a unique editing domain from archaebacteria

The N-terminal module of an archaebacterial threonyl-tRNA synthetase responsible for editing function has been crystallized in P3₁₍₂₎21 space group.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of conjugated bile salt hydrolase from Bifidobacterium longum

Two different crystal forms have been obtained of the conjugated bile salt hydrolase from B. longum and their preliminary crystallographic characterization has been carried out.

Crystals of X29, a Xenopus laevis U8 snoRNA-binding protein with nuclear decapping activity

X29, a nuclear Nudix hydrolase that binds and decaps U8 snoRNA, has been expressed in high yield and crystallized in a form that diffracts to 2.1 Å resolution.

Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins

A solubility screen for determining the best solvent condition for a particular protein prior to crystallization trials is presented.

A preliminary solubility screen used to improve crystallization trials: crystallization and preliminary X-ray structure determination of Aeropyrum pernix flap endonuclease-1

A solubility screen has been utilized to optimize initial crystallization results of A. pernix flap endonuclease-1.

APRV – a program for automated data processing, refinement and visualization

APRV is a program that automates routine procedures in high-throughput protein–ligand complex structure determination.

MAD phasing: choosing the most informative wavelength combination

An algorithm for predicting the most informative wavelength combination in the MAD case is described.

Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 Å resolution

The X-ray crystal structure of D-ribulose 5-phosphate 3-epimerase (RPE) from Synechocystis reveals that the enzyme shares a highly conserved active site with other RPEs.

CLIMS: Crystallography Laboratory Information Management System

CLIMS is a laboratory-information management system for protein crystallography that features a novel graphical interface to a relational database and assists all aspects of protein crystallization projects.

Two orthorhombic crystal structures of a galactose-specific lectin from Artocarpus hirsuta in complex with methyl-α-D-galactose. Addendum

Addendum to the paper by Rao et al. (2004), Acta Cryst. D60, 1404–1412.