Structure of thermolysin refined at 1.6 A resolution.

@article{Holmes1982StructureOT,
  title={Structure of thermolysin refined at 1.6 A resolution.},
  author={M. Holmes and B. Matthews},
  journal={Journal of molecular biology},
  year={1982},
  volume={160 4},
  pages={
          623-39
        }
}
Abstract The structure of the thermostable protease thermolysin has been refined by a restrained least-squares procedure at a nominal resolution of 1.6 A to a conventional R-value of 21.3% for 34,671 observed reflections (or R = 19.5% for reflections with F0 > 3σ(F0)). The refined structure was constrained to adhere to known stereochemistry, with root-mean-square deviations of 0.021 A from ideal bond lengths and 2.9 ° from ideal bond angles. The final model included 173 solvent molecules, which… Expand
Structure of ubiquitin refined at 1.8 A resolution.
TLDR
The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure and features a number of unusual secondary structural features, including a parallel G1 beta-bulge, two reverse Asx turns, and a symmetrical hydrogen-bonding region that involves the two helices and two of the reverse turns. Expand
Structure of papain refined at 1.65 A resolution.
TLDR
The crystal structure of papain, in which the sulfhydryl group was oxidized, was refined by a restrained least-squares procedure and it was found that the point of minimum disorder is near the molecular centroid. Expand
Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution.
TLDR
The structure of the lysozyme from bacteriophage T4 has been refined at 1.7 A resolution to a crystallographic residual of 19.3% and it is confirmed that the molecule as initially derived from a 2.4 A resolution electron density map is confirmed. Expand
Refinement of the crystal structure of wheat germ agglutinin isolectin 2 at 1.8 A resolution.
  • C. Wright
  • Chemistry, Medicine
  • Journal of molecular biology
  • 1987
TLDR
The crystal structure of wheat germ agglutinin isolectin 2 has been refined by the restrained least-squares method of Hendrickson & Konnert (1980) and side-chains involved in hydrogen bonds were found to be relatively flexible and able to adapt their conformation to changes in environment. Expand
Structure of azurin from Alcaligenes denitrificans refinement at 1.8 A resolution and comparison of the two crystallographically independent molecules.
  • E. Baker
  • Chemistry, Medicine
  • Journal of molecular biology
  • 1988
TLDR
Refinement has confirmed that the copper co-ordination is best described as distorted trigonal planar, with strong in-plane bonds to His46 NDelta 1, His117 N delta 1 and Cys112 S gamma, and much weaker axial interactions with Met121 S delta and Gly45 C = O. Expand
Crystal structure of neutral protease from Bacillus cereus refined at 3.0 A resolution and comparison with the homologous but more thermostable enzyme thermolysin.
TLDR
There appear to be no contributions to the enhanced thermostability of thermolysin from additional salt bridges, whereas contributions in the form of extra hydrogen bonding interactions could be important. Expand
Crystallographic structural analysis of phosphoramidates as inhibitors and transition-state analogs of thermolysin.
TLDR
Observed observations provide additional evidence in support of the participation of pentacoordinate intermediates in the mechanism of action of thermolysin and appear to be a better transition-state analog than is phosphoramidon. Expand
Structural analysis of the inhibition of thermolysin by an active-site-directed irreversible inhibitor.
TLDR
It appears that steric hindrance prevents the direct attack of Glu-143 on the carbonyl carbon of an extended substrate, therefore ruling out the anhydride pathway in thermolysin-catalyzed hydrolysis of polypeptide substrates and their ester analogues. Expand
Structure of Peptide Deformylase and Identification of the Substrate Binding Site*
TLDR
The structure of the Ni2+ enzyme is solved by x-ray crystallography and the hydrogen bond network stabilizing the active site involves nearly all conserved amino acid residues and well defined water molecules, one of which ligates to the tetrahedrally coordinated Ni1+ion. Expand
Preliminary X-ray crystallographic analysis of thermolysin in the presence of 4 M NaCl.
TLDR
A new method is developed to introduce 4 M NaCl into the P6(1)22 crystal of thermolysin originally grown without NaCl, and the crystal obtained by this method diffracted X-rays to 2.43 A. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 25 REFERENCES
Protein structure refinement: Streptomyces griseus serine protease A at 1.8 A resolution.
TLDR
The algorithm used for this refinement allows for the simultaneous restraint on bond distances and distances related to interbond angles, the coplanarity of atoms in planar groups, the conservation of chirality of asymmetric centres, non-bonded contact distances, conformational torsional angles and individual isotropic temperature factors. Expand
The conformation of thermolysin.
TLDR
It is suggested that the enhanced stability of thermostable proteins relative to thermolabile ones cannot be attributed to a common determinant such as metal ion or hydrophobic stabilization, but in a given instance may be due to rather subtle differences inhydrophobic character, metal binding, hydrogen bonding, ionic interactions, or a combination of all of these. Expand
The structure of thermolysin: an electron density map at 2-3 A resolution.
TLDR
The electron density map, when combined with the amino-acid sequence determined by Titani, Hermodson, Ericsson, Walsh & Neurath (1972) , revealed the conformation of the thermolysin molecule in considerable detail. Expand
Structure of crystalline -chymotrypsin. V. The atomic structure of tosyl- -chymotrypsin at 2 A resolution.
Abstract Refined atomic co-ordinates for tosyl-α-chymotrypsin have been obtained by computational refinement of co-ordinates derived from a carefully built atomic model. The two independent views ofExpand
Water structure in a protein crystal: rubredoxin at 1.2 A resolution.
TLDR
The model for rubredoxin based on X-ray diffraction data has been extensively refined with a 1.2 A resolution data set and the most tightly bound water oxygen atoms are hydrogen bonded to two or more main-chain nitrogen or oxygen atoms. Expand
The crystal structure of myoglobin: Phase determination to a resolution of 2 Å by the method of isomorphous replacement
The method of multiple isomorphous replacement has been used to solve the structure of the protein myoglobin to a resolution of 2 A. EDSAC II has been programmed to calculate the phase angles, andExpand
Dynamic information from protein crystallography. An analysis of temperature factors from refinement of the hen egg-white lysozyme structure.
TLDR
Although this analysis at a single temperature cannot establish whether thermal motion or static disorder (including conformational variability) underlies the observed effects, it suggests that the accurate determination of temperature factors will be useful in detailed studies of the dynamic properties of macromolecules. Expand
A crystallographic study of the complex of phosphoramidon with thermolysin. A model for the presumed catalytic transition state and for the binding of extended substances.
TLDR
The observed binding of phosphoramidon to thermolysin provides further evidence supporting the mechanism in which Glu143 acts as a general base, promoting the attack of water on the carbonyl carbon, rather than the alternative mechanism inWhich GLU143 attacks the carbonicl carbon directly, forming an anhydride intermediate. Expand
Molecular basis of thermostability in the lysozyme from bacteriophage T4
TLDR
The structure of a temperature sensitive (ts) mutant of T4 phage lysozyme is reported, allowing the first direct comparison of two protein structures in which all differences are directly related to a change in thermal stability. Expand
The refined crystal structure of bovine beta-trypsin at 1.8 A resolution. II. Crystallographic refinement, calcium binding site, benzamidine binding site and active site at pH 7.0.
TLDR
The crystal structure of benzamidine-inhibited bovine β -trypsin has been refined by constrained crystallographic refinement at 1·8 A resolution and led to the finding of a single site occupied by calcium. Expand
...
1
2
3
...