PDBsum entry 1hf4

Hydrolase

PDB id: 1hf4

Contents

Protein chains

129 a.a. *

Ligands

NO3 ×8

Metals

_NA ×2

Waters ×251

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural effects of monovalent anions on polymorphic lysozyme crystals.

Authors

M.C.Vaney, I.Broutin, P.Retailleau, A.Douangamath, S.Lafont, C.Hamiaux, T.Prangé, A.Ducruix, M.Riès-Kautt.

Ref.

Acta Crystallogr D Biol Crystallogr, 2001, 57, 929-940. [DOI no: 10.1107/S0907444901004504]

PubMed id

11418760

Abstract

Understanding direct salt effects on protein crystal polymorphism is addressed by comparing different crystal forms (triclinic, monoclinic, tetragonal and orthorhombic) for hen, turkey, bob white quail and human lysozymes. Four new structures of hen egg-white lysozyme are reported: crystals grown in the presence of NapTS diffracted to 1.85 A, of NaI to 1.6 A, of NaNO(3) to 1.45 A and of KSCN to 1.63 A. These new structures are compared with previously published structures in order to draw a mapping of the surface of different lysozymes interacting with monovalent anions, such as nitrate, chloride, iodide, bromide and thiocyanate. An analysis of the structural sites of these anions in the various lysozyme structures is presented. This study shows common anion sites whatever the crystal form and the chemical nature of anions, while others seem specific to a given geometry and a particular charge environment induced by the crystal packing.

Figure 4.
Figure 4 R.m.s. deviations versus the sequence number between the two independent molecules of the HEWL/NaI monoclinic structure showing the non-equivalence of loops 65-75.

Figure 6.
Figure 6 All anionic sites (red numbers) aligned on the lysozyme sequence. The unique sites are labelled according to the chemical formula of the anion taken from the corresponding PDB file.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 929-940) copyright 2001.

Secondary reference #1

Title

Novel approach to phasing proteins: derivatization by short cryo-Soaking with halides.

Authors

Z.Dauter, M.Dauter, K.R.Rajashankar.

Ref.

Acta Crystallogr D Biol Crystallogr, 2000, 56, 232-237. [DOI no: 10.1107/S0907444999016352]

PubMed id

10666615

Figure 2.
Figure 2 The refined occupancies of ten strongest (a) bromide and (b) iodide sites in the four test structures.

Figure 3.
Figure 3 The environment of halides in protein structures. The anomalous difference density is also shown at 5 . (a) and (b) Bromide ions in RNAase A near the arginine side chains, (c) iodide ion coordinated by two asparagine NH[2] groups at the surface of xylanase and (d) iodide ion located in a hydrophobic niche and hydrogen bonded to a main-chain amide of xylanase.

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

Secondary reference #2

Title

Anomalous signal of solvent bromides used for phasing of lysozyme.

Authors

Z.Dauter, M.Dauter.

Ref.

J Mol Biol, 1999, 289, 93. [DOI no: 10.1006/jmbi.1999.2744]

PubMed id

10339408

Figure 1.
Figure 1. The jdeltaF anom j/F ratio for four data sets as a function of resolution.

Figure 2.
Figure 2. The anomalous difference map contoured at 5s showing six bromide sites around the molecule of lyso- zyme. In addition, three sulfur atoms also show an anomalous signal at this level of the map.

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

Secondary reference #3

Title

Refinement of triclinic hen egg-White lysozyme at atomic resolution.

Authors

M.A.Walsh, T.R.Schneider, L.C.Sieker, Z.Dauter, V.S.Lamzin, K.S.Wilson.

Ref.

Acta Crystallogr D Biol Crystallogr, 1998, 54, 522-546. [DOI no: 10.1107/S0907444997013656]

PubMed id

9761848

Figure 7.
Fig. 7. ORTEP drawings (20% ellipsoids) of Trp62 in ( a ) LTL and ( b ) RTL; ( c ) main-chain disorder at 113±115 in LTL, only CB atoms of side chains are shown for clarity. ( d ) Main/side-chain disorder at Thr43 in LTL. The ®gures were produced using the program ORTEX (McArdle, 1994).

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #4

Title

Structures of monoclinic lysozyme iodide at 1.6 a and of triclinic lysozyme nitrate at 1.1 a.

Author

L.K.Steinrauf.

Ref.

Acta Crystallogr D Biol Crystallogr, 1998, 54, 767-780. [DOI no: 10.1107/S0907444997016922]

PubMed id

9757091

Figure 1.
Fig. 1. Ribbon drawings of lysozyme A and lysozyme B superimposed. The two molecules coincide except for the 65-75 loop.

Figure 2.
Fig. 2. (a) Lysozyme A (solid lines) in the vicinity of iodide 3. (b) Lysozyme B (solid lines) in the vicinity of iodide 7 which is the equivalent of iodide 3. Neighbors are in dotted lines. The smaller sphere in Fig. l(a) is iodide 12 which has no counterpart.

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

Secondary reference #5

Title

Locations of bromide ions in tetragonal lysozyme crystals.

Authors

K.Lim, A.Nadarajah, E.L.Forsythe, M.L.Pusey.

Ref.

Acta Crystallogr D Biol Crystallogr, 1998, 54, 899-904. [DOI no: 10.1107/S0907444998002844]

PubMed id

9757106

Figure 3.
Fig. 3. Stereo image of the Hal5 site. Given its relatively small peak in the electron-density difference map (~5a), the location of a bromide ion here is not certain and is assigned to a water molecule in the refined structure. However, other evidence suggests that this is indeed a valid anion-binding sitc for lysozyme (see text).

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #6

Title

High-Resolution structure (1.33 a) of a hew lysozyme tetragonal crystal grown in the apcf apparatus. Data and structural comparison with a crystal grown under microgravity from spacehab-01 mission.

Authors

M.C.Vaney, S.Maignan, M.Riès-Kautt, A.Ducriux.

Ref.

Acta Crystallogr D Biol Crystallogr, 1996, 52, 505-517. [DOI no: 10.1107/S090744499501674X]

PubMed id

15299672

Figure 4.
Fig. 4. Stereoview of the overall lysozyme ground structure. The Na + ion is located inside the loop 60-73 and the interactions are symolized by the dashed lines. The CI- on is localized at the interface of two molecules and is at a distance of about 24/k from the Na + ion for ground and space structures). All the diagrams were prodced using the program MOLSCRIPT (Kraulis, 1991).

Figure 6.
ig. 6. Stereoscopic views for the ground structure of the final 1Fol -IFcl electron-density ap at 1.33/~ resolution with the contour level at ltr: the issing density is observed round some atoms of the esidue Trp62 while the high quality of the map shows the quasi-atomic resolution round residue Trp63. The space struture shows similar conformations and qualities of he map.

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