Enhanced Diffractivity of Phosphoglucomutase Crystals. Use of an Alternative Cryocrystallographic Procedure

Wj, Ray; Baranidharan, S.; Y, Liu

doi:10.1107/s0907444997000887

Cited by 5 publications

(5 citation statements)

References 10 publications

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“…A continuous version of the previous desalting procedure (Ray et al, 1991) was used for this replacement (Ray et al, 1997). A continuous version of the previous desalting procedure (Ray et al, 1991) was used for this replacement (Ray et al, 1997).…”

Section: Crystalsmentioning

confidence: 99%

“…Powell energy minimization and B-factor refinement using the higher resolution (253 K) data set described in the preceding paper (6-2.4/~: Table 2, Ray, Baranidharan & Liu, 1997); simulated annealing, Powell energy minimization, and B-factor refinement as in step 2: final R factor = 23%. Manual changes in loops and side chains based on a 2Fobs-Fcaic map with model phases.…”

Section: Model Refinementmentioning

confidence: 99%

“…In this initial ED.P-6-Glc-1-P complex, the 1-and 6-phosphate groups are bound, respectively, at the proximal or phosphatetransfer subsite and at the distal or phosphate-binding subsite of the enzyme (Ray, Burgner& Post, 1990). Later, when it became possible to collect higher resolution data (Ray, Baranidharan & Liu, 1997), the revised model was incorporated into the asymmetric unit as two independent monomers? In the second complex, ED.P-1-Glc-6-P, the positions of the 1-and 6-phosphate groups are reversed (Ray, Post, Liu & Rhyu, 1993).…”

Section: Introductionmentioning

confidence: 99%

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Structure of Rabbit Muscle Phosphoglucomutase Refined at 2.4 Å Resolution

Liu

Ray²,

Baranidharan³

1997

Acta Crystallogr D Biol Crystallogr

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Data between 6.0 and 2.4 A resolution, collected at 253 K, wer used to refine a revised atomic model of muscle phosphoglucomutase: final crystallographic R factor = 16.3% (Rfree = 19.1%); final r.m.s. deviations from ideal bond lengths and angles = 0.018 A and 3.2 degrees, respectively. Features of the protein that were recognized only in the revised model include: the disposition of water molecules within domain-domain interfaces; two ion pairs buried in domain-domain interfaces, one of which is a structural arginine around which the active-site phosphoserine loop is wound; the basic architecture of the active-site 'crevice', which is a groove in a 1(1/3)-turn helix, open at both ends, that is produced by the interfacing of the four domains; the distorted hexacoordinate ligand sphere of the active-site Mg2+, where the enzymic phosphate group acts as a bidentate ligand; a pair of arginine residues in domain IV that form part of the enzymic phosphate-binding site (distal subsite) whose disposition in the two monomers of the asymmetric unit is affected unequally by distant crystallographic contacts; structural differences throughout domain IV, produced by these differing contacts, that may mimic solution differences induced by substrate binding; large differences in individually refined Debye-Waller thermal factors for corresponding main-chain atoms in monomers (1) and (2), suggesting a dynamic disorder within the crystal that may involve domain-size groups of residues; and a 'nucleophilic elbow' in the active site that resides in a topological environment differing from previous descriptions of this type of structure in other proteins.

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Section: Crystalsmentioning

confidence: 99%

Section: Model Refinementmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Structure of Rabbit Muscle Phosphoglucomutase Refined at 2.4 Å Resolution

Liu

Ray²,

Baranidharan³

1997

Acta Crystallogr D Biol Crystallogr

Self Cite

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“…Replacing the salt within crystals by PEG has occasionally been shown to be a valid strategy to preserve diffraction quality following flash-cooling (Ray et al, 1991(Ray et al, , 1997. Unfortunately, we could not find conditions that allowed ORFV CBP crystals to be transferred from 1.8 M ammonium citrate to PEG without damaging the crystals.…”

Section: Resultsmentioning

confidence: 85%

Crystallization and preliminary X-ray analysis of the chemokine-binding protein from orf virus (Poxviridae)

et al. 2010

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The parapoxvirus orf virus (ORFV) encodes a chemokine-binding protein (CBP) that functions to downregulate the host's immune response at the site of infection by blocking the chemokine-induced recruitment of immune cells. In order to shed light on the structural determinants of CBP-chemokine binding, ORFV CBP was crystallized as part of an ongoing structure-function study on this protein. ORFV CBP crystals were obtained by the sitting-drop vapour-diffusion technique using ammonium citrate as a precipitant. The crystal quality was greatly improved through the addition of small-molecule additives to the crystallization mother liquor. ORFV CBP crystals diffracted X-rays to 2.50 A resolution and belonged to the hexagonal space group P6(1)22 or its enantiomorph P6(5)22, with unit-cell parameters a = b = 75.62, c = 282.49 A, alpha = 90, beta = 90, gamma = 120 degrees.

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“…If the crystals do not react well to a sudden change of solvent, a¯ow cell can be used. For instance, in the study of phosphoglucomutase, 2 M ammonium sulfate and PEG 3350 was replaced over many hours in a¯ow cell by PEG 600 (Ray et al, 1997). A decrease in mosaic spread and an improvement of the diffraction limit from 2.75 to 2.35 A Ê was observed.…”

Section: Cryo-solutionsmentioning

confidence: 99%

Cool data: quantity AND quality

Garman

1999

Acta Crystallogr D Biol Cryst

155

142

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The use of cryo-techniques in macromolecular crystallography has increased enormously over the last eight years and has become a vital part of modern X-ray data-collection methods. This paper presents some reasons for the rise in popularity of cryo-techniques and a brief outline of the basic methods, followed by a detailed discussion of factors to be considered when trying to optimize both the quantity and quality of the data collected. As more experimenters at synchrotrons observe significant radiation damage to crystals held near 100 K, the available options for further prolonging crystal lifetime and extending the techniques become worth investigating. Some possibilities and parameters to be considered are presented, although these must remain speculative until more experimental data are available.

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Enhanced Diffractivity of Phosphoglucomutase Crystals. Use of an Alternative Cryocrystallographic Procedure

Cited by 5 publications

References 10 publications

Structure of Rabbit Muscle Phosphoglucomutase Refined at 2.4 Å Resolution

Structure of Rabbit Muscle Phosphoglucomutase Refined at 2.4 Å Resolution

Crystallization and preliminary X-ray analysis of the chemokine-binding protein from orf virus (Poxviridae)

Cool data: quantity AND quality

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