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X-ray structure of monoclinic turkey egg lysozyme at 1.3 A resolution.

Harata K
Acta Crystallogr D Biol Crystallogr 49 497-504 (1993)
Cited: 34 times
EuropePMC logo PMID: 15299509

Abstract

Monoclinic crystals of turkey egg lysozyme (TEL, E.C. 3.2.1.17) were obtained from 2.2 M ammonium sulfate solution at pH 4.2. They belong to space group P2(1) with unit-cell dimensions a = 38.07, b = 33.20, c = 46.12 A and beta = 110.1 degrees, and contain one molecule in the asymmetric unit (V(m) = 1.91 A(3) Da(-1)). The three-dimensional structure of TEL was solved by the method of multiple isomorphous replacement with anomalous scattering. Area detector data to 1.5 A resolution from native and heavy-atom derivatives were used for the structure determination. The structure was refined by the simulated-annealing method with diffraction data of 10-1.30 A resolution. The conventional R factor was 0.189. The root-mean-square deviations from ideal bond distances and angles were 0.016 A and 2.9 degrees, respectively. The backbone structure of TEL is very similar to that of hen egg lysozyme (HEL) and the difference in seven amino-acid residues does not affect the basic folding of the polypeptide chain. Except for the region from Gly101 to Gly104, the geometry of the active-site cleft is conserved between TEL and HEL. The Gly101 residue is located at the end of the sugar-binding site and the structural change in this region between TEL and HEL is considered to be responsible for the difference in their enzymatic properties.

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  2. Force Field for Peptides and Proteins based on the Classical Drude Oscillator. Lopes PE, Huang J, Shim J, Luo Y, Li H, Roux B, Mackerell AD. J Chem Theory Comput 9 5430-5449 (2013)
  3. LigASite--a database of biologically relevant binding sites in proteins with known apo-structures. Dessailly BH, Lensink MF, Orengo CA, Wodak SJ. Nucleic Acids Res. 36 D667-73 (2008)
  4. Peptide-plane flipping in proteins. Hayward S. Protein Sci. 10 2219-2227 (2001)
  5. A priori prediction of adsorption isotherm parameters and chromatographic behavior in ion-exchange systems. Ladiwala A, Rege K, Breneman CM, Cramer SM. Proc Natl Acad Sci U S A 102 11710-11715 (2005)
  6. Modeling of loops in proteins: a multi-method approach. Jamroz M, Kolinski A. BMC Struct. Biol. 10 5 (2010)
  7. Current status of protein force fields for molecular dynamics simulations. Lopes PE, Guvench O, MacKerell AD. Methods Mol. Biol. 1215 47-71 (2015)
  8. Long-range distance measurements in proteins at physiological temperatures using saturation recovery EPR spectroscopy. Yang Z, Jiménez-Osés G, López CJ, Bridges MD, Houk KN, Hubbell WL. J. Am. Chem. Soc. 136 15356-15365 (2014)
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  10. ResBoost: characterizing and predicting catalytic residues in enzymes. Alterovitz R, Arvey A, Sankararaman S, Dallett C, Freund Y, Sjölander K. BMC Bioinformatics 10 197 (2009)
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  12. Mapping hydrophobicity on the protein molecular surface at atom-level resolution. Nicolau DV, Paszek E, Fulga F, Nicolau DV. PLoS One 9 e114042 (2014)
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  14. New Deep Learning Methods for Protein Loop Modeling. Nguyen SP, Li Z, Xu D, Shang Y. IEEE/ACM Trans Comput Biol Bioinform 16 596-606 (2019)
  15. Protein molecular surface mapped at different geometrical resolutions. Nicolau DV, Paszek E, Fulga F, Nicolau DV. PLoS One 8 e58896 (2013)
  16. The pressure-temperature phase diagram of hen lysozyme at low pH. Maeno A, Matsuo H, Akasaka K. Biophysics (Nagoya-shi) 5 1-9 (2009)
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  19. Prediction of protein pK a with representation learning. Gokcan H, Isayev O. Chem Sci 13 2462-2474 (2022)
  20. Towards comprehensive analysis of protein family quantitative stability-flexibility relationships using homology models. Verma D, Guo JT, Jacobs DJ, Livesay DR. Methods Mol Biol 1084 239-254 (2014)


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  2. Very fast empirical prediction and rationalization of protein pKa values. Li H, Robertson AD, Jensen JH. Proteins 61 704-721 (2005)
  3. Packing at the protein-water interface. Gerstein M, Chothia C. Proc. Natl. Acad. Sci. U.S.A. 93 10167-10172 (1996)
  4. Crystal structures of guinea-pig, goat and bovine alpha-lactalbumin highlight the enhanced conformational flexibility of regions that are significant for its action in lactose synthase. Pike AC, Brew K, Acharya KR. Structure 4 691-703 (1996)
  5. Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1. Braden BC, Souchon H, Eiselé JL, Bentley GA, Bhat TN, Navaza J, Poljak RJ. J. Mol. Biol. 243 767-781 (1994)
  6. Three-dimensional structure analysis of PROSITE patterns. Kasuya A, Thornton JM. J. Mol. Biol. 286 1673-1691 (1999)
  7. Design and structural analysis of an engineered thermostable chicken lysozyme. Shih P, Kirsch JF. Protein Sci. 4 2063-2072 (1995)
  8. Crystal structure of a phage library-derived single-chain Fv fragment complexed with turkey egg-white lysozyme at 2.0 A resolution. Aÿ J, Keitel T, Küttner G, Wessner H, Scholz C, Hahn M, Höhne W. J. Mol. Biol. 301 239-246 (2000)
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  10. Solution structure of biopolymers: a new method of constructing a bead model. Banachowicz E, Gapiński J, Patkowski A. Biophys. J. 78 70-78 (2000)
  11. Crystal structures of pheasant and guinea fowl egg-white lysozymes. Lescar J, Souchon H, Alzari PM. Protein Sci. 3 788-798 (1994)
  12. Solid-phase polyethylene glycol conjugation using hydrophobic interaction chromatography. Niu J, Zhu Y, Xie Y, Song L, Shi L, Lan J, Liu B, Li X, Huang Z. J Chromatogr A 1327 66-72 (2014)
  13. Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein. Zhang P, Yang W. J Chem Phys 159 024118 (2023)


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