<i>OASIS</i>: a computer program for breaking phase ambiguity in one-wavelength anomalous scattering or single isomorphous substitution (replacement) data

Hao, Quan; Gu, Yueliang; Zheng, Chao; Hai-Fu, Fan

doi:10.1107/s0021889800001424

Cited by 64 publications

(54 citation statements)

References 9 publications

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“…Moreover, use of the powerful solvent-¯attening programs DM (Cowtan, 1994) and SOLOMON (Abrahams & Leslie, 1996) did not signi®cantly improve this. Attempts to use different approaches to partial structure re®nement and phase-probability distribution calculation, such as those available in the programs MLPHARE (Otwinowski, 1991) and OASIS (Hao et al, 2000), were no more successful. It therefore seemed that with the programs currently available, the combination of a very low anomalous signal (1%) and relatively low resolution data (d min = 2.5 A Ê ) the determination of the sulfur substructure would not allow full phasing of a crystal structure.…”

Section: Phasing Model Building and Refinementmentioning

confidence: 99%

The C₁subunit of α-crustacyanin: thede novophasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods

Gordón

Leonard

McSweeney

et al. 2001

Acta Crystallogr D Biol Cryst

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The previously unknown crystal structure of the C1 subunit of the carotenoid‐binding protein α‐crustacyanin has been determined using the anomalous scattering available at 1.77 Å wavelength to determine the partial structure of the S atoms intrinsic to the native protein. The resulting `heavy‐atom' phases, in conjunction with near‐atomic resolution (dmin = 1.15 Å) data, were then used to initiate successful structure determination using a direct‐methods approach. This is, to the authors' knowledge, the first time such a small anomalous signal (∼1%) has been used to aid the determination of a macromolecular structure. As well as the structure itself, the methods used during data collection and those used in the elucidation of the sulfur `heavy‐atom' partial structure are described here. As predicted, the C1 subunit adopts a tertiary structure typical of the lipocalin superfamily: an eight‐stranded antiparallel β‐barrel with a repeated +1 topology. The β‐barrel has a calyx shape with the two molecules in the asymmetric unit interacting in such a way that the open ends of each calyx face each other, although they do not form a single elongated pocket. A comparison of this structure with those of other members of the lipocalin superfamily has allowed speculation as to the nature of carotenoid binding by the protein.

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Section: Phasing Model Building and Refinementmentioning

confidence: 99%

The C₁subunit of α-crustacyanin: thede novophasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods

Gordón

Leonard

McSweeney

et al. 2001

Acta Crystallogr D Biol Cryst

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“…The crystal structure of GtfA was determined using single-wavelength anomalous dispersion phasing (27) method from a single SeMet-substituted protein crystal to a highest resolution of 2.3 Å. The SHELXD program (28) implemented in IPCAS was used to locate the heavy atoms, and the phase was calculated by OASIS (29) and further improved with the programs RESOLVE and Buccaneer (30 -32). Electron density maps showed clear features of secondary structural elements.…”

Section: Methodsmentioning

confidence: 99%

Structure of a Novel O-Linked N-Acetyl-d-glucosamine (O-GlcNAc) Transferase, GtfA, Reveals Insights into the Glycosylation of Pneumococcal Serine-rich Repeat Adhesins

Shi

Jiang

Zhu

et al. 2014

Journal of Biological Chemistry

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Background: O-GlcNAcylation of surface adhesin PsrP catalyzed by GtfA-GtfB complex is involved in the pathogenicity of Streptococcus pneumoniae. Results: The crystal structure of GtfA reveals a novel O-GlcNAc transferase with a ␤-meander "add-on" domain. Conclusion:The add-on domain is crucial for complex formation and acceptor recognition. Significance: The structure provides insights into the catalytic mechanism of a novel bacterial O-GlcNAc transferase.

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“…Improved synchrotron beamlines equipped with CCD or imaging-plate detectors as well as modern data-processing software can very accurately estimate re¯ection intensities and their uncertainties. Direct-methods programs based on the shake-and-bake principle (SnB, Smith et al, 1998;SHELXD, Sheldrick, 1998) for ®nding anomalous scatterer positions and powerful phasing algorithms, especially those based on maximum likelihood (SHARP, de La Fortelle & Bricogne, 1997;MLPHARE, Otwinowski, 1991) or direct methods (OASIS; Hao et al, 2000), often lead to rapid and easy structure solution.…”

Section: Introductionmentioning

confidence: 99%

Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy

Dauter

Adamiak

2001

Acta Crystallogr D Biol Crystallogr

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The crystal structure of a left-handed Z-DNA hexamer duplex d(CGCGCG) 2 has been solved based on the anomalous diffraction signal of inherent P atoms using data collected at the single wavelength of 1.54 A Ê . The anomalous signal of about 2% of the total diffracted intensity, constant for all nucleic acids, may be generally useful for solving crystal structures of DNA and RNA oligomers. The multiplicity of intensity measurements is shown to crucially affect the data quality and the ability to solve the phase problem. The anisotropic model re®ned to an R factor of 8.9% at 0.95 A Ê resolution.

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OASIS: a computer program for breaking phase ambiguity in one-wavelength anomalous scattering or single isomorphous substitution (replacement) data

Cited by 64 publications

References 9 publications

The C₁subunit of α-crustacyanin: thede novophasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods

The C₁subunit of α-crustacyanin: thede novophasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods

Structure of a Novel O-Linked N-Acetyl-d-glucosamine (O-GlcNAc) Transferase, GtfA, Reveals Insights into the Glycosylation of Pneumococcal Serine-rich Repeat Adhesins

Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy

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OASIS: a computer program for breaking phase ambiguity in one-wavelength anomalous scattering or single isomorphous substitution (replacement) data

Cited by 64 publications

References 9 publications

The C1subunit of α-crustacyanin: thede novophasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods

The C1subunit of α-crustacyanin: thede novophasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods

Structure of a Novel O-Linked N-Acetyl-d-glucosamine (O-GlcNAc) Transferase, GtfA, Reveals Insights into the Glycosylation of Pneumococcal Serine-rich Repeat Adhesins

Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy

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The C₁subunit of α-crustacyanin: thede novophasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods

The C₁subunit of α-crustacyanin: thede novophasing of the crystal structure of a 40 kDa homodimeric protein using the anomalous scattering from S atoms combined with direct methods