PDBsum entry 1yyf

Chaperone/hydrolase

PDB id: 1yyf

Contents

Protein chains

408 a.a.

180 a.a.

Ligands

ADP ×2

References listed in PDB file

Key reference

Title

Correction of X-Ray intensities from an hslv-Hslu co-Crystal containing lattice-Translocation defects.

Authors

J.Wang, S.H.Rho, H.H.Park, S.H.Eom.

Ref.

Acta Crystallogr D Biol Crystallogr, 2005, 61, 932-941. [DOI no: 10.1107/S0907444905009546]

PubMed id

15983416

Abstract

Because of lattice-translocation defects, two identical but translated lattices can coexist as a single coherent mosaic block in a crystal. The observed structure in such cases is a weighted sum of two identical but translated structures, one from each lattice; the observed structure factors are a weighted vector sum of the structure factors with identical unit amplitudes but shifted phases. The correction of X-ray intensities from a single crystal containing these defects of the hybrid HslV-HslU complex, which consists of Escherichia coli HslU and Bacillus subtilis HslV (also known as CodW), is reported. When intensities are not corrected, a biologically irrelevant complex (with CodW from one lattice and HslU from another) is implied to exist. Only upon correction does a biologically functional CodW-HslU complex structure emerge.

Figure 1.
Figure 1 Observed alternating sharp-diffuse reflections. In the l direction, strong reflections are observed beyond 4.0 Å (large concentral circles) and some reflections are observed at 3.6 Å (reflections with small circles); in the h and k directions reflections barely pass 4.5 Å. Only the third of the reflections with index l = 3n (boxed) have typical Bragg spots and the remaining reflections have streaky features along the l direction. Data were processed to 4.16 Å, slightly below an ice ring at 4.15 Å.

Figure 6.
Figure 6 Incorrect model containing an extra HslV particle (magenta) at (0, 0, 1/3) fits the uncorrected observed data better than the correct model.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 932-941) copyright 2005.

Secondary reference #1

Title

Correction of X-Ray intensities from single crystals containing lattice-Translocation defects.

Authors

J.Wang, S.Kamtekar, A.J.Berman, T.A.Steitz.

Ref.

Acta Crystallogr D Biol Crystallogr, 2005, 61, 67-74. [DOI no: 10.1107/S0907444904026721]

PubMed id

15608377

Figure 6.
Figure 6 Reciprocal-space lattice in the presence of the lattice-translocation defect of Fig. 3-with z = 1/2. When the defect occurs with low frequency ( < 5%), the streaky features are limited to slightly elliptically shaped lattice points. Such a limited defect can be partially corrected during intensity integration using an elliptical spot-shape option when the crystal is rotated along the a* axis during data collection, but it cannot when the axis of the crystal rotation is perpendicular to a*. In the latter case, streaky features would appear only in one orientation and many extra Bragg reflections would not be predictable with a standard definition of the mosaicity in a second orientation that is 90° away from the first orientation.

Figure 7.
Figure 7 An experimental electron-density map of 29 DNA polymerase at 2.5 Å using phases initially derived from Hg derivatives after their X-ray intensities were corrected, followed by density modification and twofold non-crystallographic symmetry averaging. This map is contoured at 1.0 and superimposed with the finally refined model.

The above figures are reproduced from the cited reference with permission from the IUCr

Secondary reference #2

Title

A second response in correcting the hslv-Hslu quaternary structure.

Author

J.Wang.

Ref.

J Struct Biol, 2003, 141, 7-8.

PubMed id

12576015

Secondary reference #3

Title

The quaternary arrangement of hslu and hslv in a cocrystal: a response to wang, Yale.

Authors

M.Bochtler, H.K.Song, C.Hartmann, R.Ramachandran, R.Huber.

Ref.

J Struct Biol, 2001, 135, 281-293. [DOI no: 10.1006/jsbi.2001.4413]

PubMed id

11722168

Secondary reference #4

Title

A corrected quaternary arrangement of the peptidase hslv and atpase hslu in a cocrystal structure.

Author

J.Wang.

Ref.

J Struct Biol, 2001, 134, 15-24. [DOI no: 10.1006/jsbi.2001.4347]

PubMed id

11469873

Secondary reference #5

Title

The structures of hsiu and the ATP-Dependent protease hsiu-Hsiv.

Authors

M.Bochtler, C.Hartmann, H.K.Song, G.P.Bourenkov, H.D.Bartunik, R.Huber.

Ref.

Nature, 2000, 403, 800-805. [DOI no: 10.1038/35001629]

PubMed id

10693812

Figure 1.
Figure 1: Summary of the three crystal forms (a-c) that were used for structure determination. Subunits in the respective asymmetric units are numbered 1-6.

Figure 2.
Figure 2: Comparison of HsIU and NSF main chains. a, Superposition of the ligand-bound (coloured) and free (white) HslU forms. Chains 1 and 2 of the P321 crystals (see Fig. 1c) are shown. The N domains (shown in green and red) have been superimposed (r.m.s.d. C bond lengths = 0.5 Å for the central -sheet, r.m.s.d. C bond lengths = 1.2 Å for the whole domain). For clarity, the N and I domains of the free form have been omitted. b, Stereo diagram of NSF D2.

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd