PDBsum entry 6svb

Hydrolase

PDB id: 6svb

Contents

Protein chain

223 a.a.

Ligands

BEN

SO4 ×2

Metals

_CA

Waters ×288

PDB id:

6svb

Name:

Hydrolase

Title:

Terahertz irradiated structure of bovine trypsin (odd frames of crystal x40)

Structure:

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

Source:

Bos taurus. Cattle. Organism_taxid: 9913

Resolution:

1.15Å R-factor: 0.138 R-free: 0.182

Authors:

V.Ahlberg Gagner,I.Lundholm,M.J.Garcia-Bonete,H.Rodilla,R.Friedman, V.Zhaunerchyk,G.Bourenkov,T.Schneider,J.Stake,G.Katona

Key ref:

V.A.Gagnér et al. (2019). Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties. Sci Rep, 9, 19281. PubMed id: 31848402 DOI: 10.1038/s41598-019-55777-5

Date:

18-Sep-19 Release date: 22-Jan-20

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: 10.1038/s41598-019-55777-5

Sci Rep 9:19281 (2019)

PubMed id: 31848402

Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties.

V.A.Gagnér, I.Lundholm, M.J.Garcia-Bonete, H.Rodilla, R.Friedman, V.Zhaunerchyk, G.Bourenkov, T.Schneider, J.Stake, G.Katona.

ABSTRACT

Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.