Protein crystallization for genomics: towards high-throughput optimization techniques

Automation of crystal optimization techniques for adaptation to high-throughput techniques is described.

MAD phasing: probabilistic estimate of |F_oa|

The probabilistic estimate of the amplitudes for normal scattering from the anomalous scattering substructure is attempted in the two-wavelength case.

Structure of product-bound Bacillus caldolyticus uracil phosphoribosyltransferase confirms ordered sequential substrate binding

The structure of uracil phosphoribosyltransferase from B. caldolyticus with bound UMP is described and a catalytic mechanism is proposed.

Structure-based enzyme inhibitor design: modeling studies and crystal structure analysis of Pneumocystis carinii di­hydrofolate reductase ternary complex with PT653 and NADPH

Structural data are reported for N-(2,4-diaminopteridin-6-yl)methyldibenz[b,f]azepine (PT653), an example of structure-based inhibitor design with 21-fold selectivity for P. carinii dihydrofolate reductase (pcDHFR) relative to rat liver dihydrofolate reductase (rlDHFR).

Structure of a domain-opened mutant (R121D) of the human lactoferrin N-lobe refined from a merohedrally twinned crystal form

The structure of the R121D mutant of the N-lobe half-molecule of human lactoferrin has been determined and refined at 3.0 Å resolution using data from a merohedrally twinned crystal form. The mutant, in its iron-free form, has a domain-opened structure that matches that of the N-lobe of full-length human lactoferrin.

High-resolution crystallographic map interpretation

A method is presented for high-resolution protein crystallographic map interpretation.

ARP/wARP's model-building algorithms. I. The main chain

Algorithms for automatic model-building in ARP/wARP.

Triiodide derivatization and combinatorial counter-ion replacement: two methods for enhancing phasing signal using laboratory Cu Kα X-ray equipment

In-house protein derivatization and structure solution using triiodide solutions is illustrated using five test cases. Also discussed is the method of combinatorial counter-ion replacement and its usefulness on conventional X-ray sources.

The three-dimensional structure of calcium-depleted human C-reactive protein from perfectly twinned crystals

The structure of calcium-depleted human C-reactive protein has been determined at 3.15 Å from perfectly twinned crystals. The structure reveals two independent pentamers which form a face-to-face decamer across a dyad near-parallel to the twinning twofold axis.

Thermolysin in the absence of substrate has an open conformation

The structure of thermolysin in the absence of substrate has been determined in a new crystal form. The enzyme takes an open conformation consistent with hinge-bending during the catalytic cycle.

Structure of pectate lyase A: comparison to other isoforms

The crystal structures of pectate lyase A from E. chrysanthemi EC16 are reported in two space groups, C2 and R3. Comparison to other pectate lyase isoforms from E. chrysanthemi is discussed.

Structure of the S pilus periplasmic chaperone SfaE at 2.2 Å resolution

The 2.2 Å crystal structure of the periplasmic chaperone SfaE is described and compared with a number of previously determined structures of homologous chaperones.

Structure of ribosomal protein L1 from Methanococcus thermolithotrophicus. Functionally important structural invariants on the L1 surface

The structure of ribosomal protein L1 from M. thermolithotrophicus compared with L1 protein structures from two other sources reveals two regions which retain their structure in all three proteins. These structural invariants are involved in intermolecular interactions in the crystals and could be treated as potential RNA-binding sites.

Cloning, expression, purification and preliminary X-ray crystallographic studies of Escherichia coli Hsp100 nucleotide-binding domain 2 (NBD2)

To investigate how NBD2 participates in ClpB function to disaggregate denatured proteins, ClpB NBD2 has been cloned and crystallized.

Crystallization and X-ray diffraction data for a new form of concanavalin A

Crystallization conditions and X-ray diffraction data for a new form of concanavalin A are described.

Crystallization and preliminary diffraction data of BaP1, a haemorrhagic metalloproteinase from Bothrops asper snake venom

BaP1, a venom haemorrhagic class P1 metalloproteinase, has been crystallized and diffraction data have been collected to 2.7 Å resolution.

Crystallization of bothrombin, a fibrinogen-converting serine protease isolated from the venom of Bothrops jararaca

Bothrombin, a serine protease which activates blood coagulation factor VIII, aggregates platelets and cleaves fibrinogen, has been crystallized and diffraction data have been collected to 2.8 Å resolution.

Expression, refolding and crystallization of Aquifex aeolicus elongation factor P

A new refolding procedure has facilitated growth of diffracting crystals of elongation factor P in the absence of contaminating oligonuleotides.

Expression, purification and crystallization of a collagen-binding fragment of Yersinia adhesin YadA

A recombinant collagen-binding fragment of adhesin YadA of Y. enterocolitica serotype O:3 has been produced in E. coli, purified and crystallized.

Towards structural understanding of feedback control of arginine biosynthesis: cloning and expression of the gene for the arginine-inhibited N-acetyl-L-glutamate kinase from Pseudomonas aeruginosa, purification and crystallization of the recombinant enzyme and preliminary X-ray studies

N-Acetyl-L-glutamate kinase from P. aeruginosa catalyses the controlling step of arginine biosynthesis and is feedback inhibited by arginine. The gene for this enzyme was cloned and expressed at high levels in E. coli. Crystals of the purified recombinant enzyme, belonging to space group P1, diffracted to a resolution of 2.75 Å.

Purification, crystallization and preliminary X-ray diffraction results of human 17β-hydroxysteroid de­hydrogenase type 5

The 17β-hydroxysteroid dehydrogenase type 5 responsible for androgen biosynthesis in peripheral tissues has now yielded high-resolution crystals.

Crystallization and preliminary crystallographic studies on the chromo shadow domain (CSD) of mouse heterochromatin protein M31

The chromo shadow domain (CSD) of the murin HP1-like protein M31 has been crystallized and X-ray diffraction data have been collected to 2.9 Å. The native crystals belong to space group C222₁ with unit-cell parameters a = 60.0, b = 95.6, c = 91.7 Å and α = β = γ = 90°

Crystallization and preliminary crystallographic analysis of acylamino-acid releasing enzyme from the hyperthermophilic archaeon Aeropyrum pernix

Crystals of acylamino acid releasing enzyme from hyperthermophilic archaeon A. pernix strain K1 have been obtained. The crystal belongs to the space group P1 with unit cell dimensions of a =107.5, b =109.9 and c =119.4 Å, α =108.1, β= 109.8 and γ = 91.9° at 2.9 Å resolution.

Purification, crystallization and X-ray analysis of swine vesicular disease virus

Crystals of the JX/78 strain of SVDV were obtained from virus in two wells of crystallization conditions and present preliminary X-ray data to 3.6 Å resolution.

Crystallization and preliminary X-ray analysis of substrate complexes of leucine de­hydrogenase from Thermoactinomyces intermedius

Leucine dehydrogenase from T. intermedius has been crystallized as a binary complex with 2-ketoisocaproate and as a non-productive ternary complex with NAD⁺ and 2-ketoisocaproate in forms suitable for structure determination.

Crystallization and preliminary X-ray crystallographic studies of the sixth PDZ domain of glutamate-receptor interacting protein 1 (GRIP1) from Rattus norvegicus

The PDZ6 domain of GRIP1 from R. norvegicus has been crystallized in the apo form and complexed with the octapeptide of the liprin-α1 C-terminus. The native and complex crystals belong to space group P6₁22 (or P6₅22) and R32 and diffracted to 1.5 and 1.8 Å, respectively.

Crystallization of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli

The ATPase domain of the membrane-anchored protease FtsH of E. coli has been crystallized and native data to 1.5 Å spacing have been collected using synchrotron radiation.

Crystallization and preliminary X-ray diffraction analysis of brefeldin A-ADP ribosylated substrate (BARS)

A truncated form of brefeldin A-ADP ribosylated substrate (residues 1–350), a protein involved in Golgi membrane fission, has been expressed, purified and crystallized. SeMet-substituted crystals were also prepared, aiming at the three-dimensional structure solution via MAD methods.

Crystallization and preliminary X-ray crystallographic analysis of enoyl-acyl carrier protein reductase from Helicobacter pylori

Enoyl-ACP reductase from H. pylori has been crystallized in the presence of its cofactor NADH and the inhibitor triclosan (or its analogue diclosan). Diffraction data have been collected to 2.5 Å (or 2.3 Å) resolution with synchrotron X-rays.

4-Chlorocatechol 1,2-dioxygenase from the chlorophenol-utilizing Gram-positive Rhodococcus opacus 1CP: crystallization and preliminary crystallographic analysis

4-Chlorocatechol 1,2-dioxygenase from the Gram-positive bacterium R. opacus (erythropolis) 1CP, an enzyme involved in the aerobic biodegradation of chloroaromatic compounds, has been crystallized. This is the first intradiol dioxygenase which specifically catalyzes the cleavage of chlorocatechols in Gram-positive bacteria to give diffraction-quality crystals.

The crystal structure of PEBP-2, a homologue of the PEBP/RKIP family

The crystal structure of a mouse phosphatidylethanolamine-binding protein homologue (mPEBP-2) has been determined to 1.8 Å. Regions of distinctive sequence associated with the PEBP-2 subset identified from alignments of the PEBP family are discussed with reference to the structure.

Elevated temperature and tyrosine iodination aid in the crystallization and structure determination of an antifreeze protein

High-temperature incubation and iodination of a specific tyrosine residue are required for crystallization and SAS structure determination of an antifreeze protein. These methods can be employed to modify other target proteins in order to aid in their crystallization and structure determination.

Handbook of metalloproteins