3OTJ

A Crystal Structure of Trypsin Complexed with BPTI (Bovine Pancreatic Trypsin Inhibitor) by X-ray/Neutron Joint Refinement

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.198 
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

X-ray and neutron protein crystallographic analysis of the trypsin-BPTI complex.

Kawamura, K., Yamada, T., Kurihara, K., Tamada, T., Kuroki, R., Tanaka, I., Takahashi, H., Niimura, N.

(2011) Acta Crystallogr.,Sect.D 67: 140-148

  • DOI: 10.1107/S0907444910053382

  • PubMed Abstract: 

    • In this work, the crystal structure of the β-trypsin-bovine pancreatic trypsin inhibitor (BPTI) complex was refined and the D and H atoms in the complex were identified using data from both 1.6 Å resolution X-ray diffraction and 2.15 Å resolution neu ...

    In this work, the crystal structure of the β-trypsin-bovine pancreatic trypsin inhibitor (BPTI) complex was refined and the D and H atoms in the complex were identified using data from both 1.6 Å resolution X-ray diffraction and 2.15 Å resolution neutron diffraction. After crystallization in an H(2)O solution, the sample crystal was soaked in a D(2)O solution for about two weeks. The protonation states of the catalytic triad (Asp102, His57 and Ser195) were observed. These results confirmed that the nucleophilic reactivity of the hydroxyl group of Ser195 was increased by forming a hydrogen bond with His57. According to structural analysis, the trypsin-BPTI interfaces located at the scissile peptide and the active sites were inaccessible to solvent water, and the amide H atoms of P2' Arg17/I, Gly216/E and Gly193/E at the binding interface were protected from H/D exchange. In contrast, both the amide H atom of P1' Ala16/I of the scissile peptide bond P1-P1' and the H atom between His57 N(ℇ2) and Ser195 O(γ) were replaced by D atoms. The hydrogen-bond networks at the S1 pocket were also confirmed and discussed from the viewpoint of substrate recognition. Moreover, the first neutron crystallographic structure of the Michaelis complex state of trypsin-BPTI is presented.

    Organizational Affiliation: 

    Institute of Applied Beam Science, Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
E
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pancreatic trypsin inhibitor
I
58Bos taurusMutation(s): 0 
Find proteins for P00974 (Bos taurus)
Go to UniProtKB:  P00974
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
E, I
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DOD
Query on DOD
Download SDF File 
Download CCD File 
E, I
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.198 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 75.604α = 90.00
b = 85.361β = 90.00
c = 122.551γ = 90.00
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.209 
Software Package:
Software NamePurpose
SCALEPACKdata scaling
nCNSphasing
nCNSrefinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-27
    Type: Data collection
  • Version 1.3: 2011-08-21
    Type: Other
  • Version 1.4: 2017-11-08
    Type: Refinement description