PDBsum entry 4i8h

Hydrolase

PDB id: 4i8h

Contents

Protein chain

223 a.a.

Ligands

BEN

SO4 ×2

GOL

Metals

_CA

Waters ×430

PDB id:

4i8h

Name:

Hydrolase

Title:

Bovine trypsin at 0.75 resolution

Structure:

Cationic trypsin. Chain: a. Synonym: beta-trypsin. Ec: 3.4.21.4

Source:

Bos taurus. Bovine,cow,domestic cattle,domestic cow. Organism_taxid: 9913

Resolution:

0.75Å R-factor: 0.102 R-free: 0.111

Authors:

Z.Dauter,D.Liebschner,M.Dauter,A.Brzuszkiewicz

Key ref:

D.Liebschner et al. (2013). On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin. Acta Crystallogr D Biol Crystallogr, 69, 1447-1462. PubMed id: 23897468 DOI: 10.1107/S0907444913009050

Date:

03-Dec-12 Release date: 19-Dec-12

Protein chain

P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus

Seq: 246 a.a.

Struc: 223 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

DOI no: 10.1107/S0907444913009050

Acta Crystallogr D Biol Crystallogr 69:1447-1462 (2013)

PubMed id: 23897468

On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin.

D.Liebschner, M.Dauter, A.Brzuszkiewicz, Z.Dauter.

ABSTRACT

Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C(α) and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 Å and more than one third were conserved within 0.1 Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments.