1R8O

Crystal structure of an unusual Kunitz-type trypsin inhibitor from Copaifera langsdorffii seeds

• PDB DOI:  https://doi.org/10.2210/pdb1R8O/pdb

• Classification: HYDROLASE INHIBITOR
• Organism(s): Copaifera langsdorffii
• Mutation(s): No 


• Deposited: 2003-10-27 Released: 2004-05-25 
• Deposition Author(s): Krauchenco, S., Nagem, R.A.P., da Silva, J.A., Marangoni, S., Polikarpov, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.212 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Three-dimensional structure of an unusual Kunitz (STI) type trypsin inhibitor from Copaifera langsdorffii.

Krauchenco, S., Nagem, R.A.P., Da Silva, J.A., Marangoni, S., Polikarpov, I.

(2004) Biochimie 86: 167-172

• PubMed: 15134830 
• DOI: https://doi.org/10.1016/j.biochi.2004.03.004
• Primary Citation of Related Structures:  
  1R8O


• PubMed Abstract: 
  

The crystallographic structure of a novel trypsin inhibitor (CTI) from Copaifera langsdorffii is reported. The structure was solved by MIRAS procedure and refined to a crystallographic residual of 17.3% (R(free) = 20.3%) at 1.8 A resolution. Two isomorphous derivatives were obtained by quick cryo-soaking approach. CTI is the first structure of a member of Kunitz (STI) family formed by two noncovalently bound polypeptide chains and only one disulfide bridge. A standard Kunitz-type inhibitor has a single polypeptide chain and two disulfide bridges. Structural features granting CTI high inhibitory activity are discussed.

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Related Citations: 

• Crystallization and preliminary X-ray diffraction analysis of a novel tryspin inhibitor from seeds of Copaifera langsdorffii
  Krauchenco, S., Silva, J.A., Nagem, R.A.P., Brando Neto, J.R., Forrer, V.P., Carmona e Ferreira, R., Macedo, M.L.R., Novello, J.C., Marangoni, S., Polikarpov, I.
  (2001) Acta Crystallogr D Biol Crystallogr 57: 1316

• Biochemical characterization and N-terminal sequences of two new trypsin inhibitors from Copaifera langsdorffii seeds
  da Silva, J.A., Macedo, M.L.R., Novello, J.C., Marangoni, S.
  (2001) J Protein Chem 20: 1

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Organizational Affiliation: 

Grupo de Cristalografia, Department of Physics and Informatics, Institute of Physics (IFSC), University of Sao Paulo, Avenue Trabalhador Saocarlense, 400, CEP 13560-970, Sao Carlos, SP, Brazil.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.03 kDa 
• Atom Count: 1,449 
• Modelled Residue Count: 167 
• Deposited Residue Count: 167 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kunitz trypsin inhibitor	A	96	Copaifera langsdorffii	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kunitz trypsin inhibitor	B	71	Copaifera langsdorffii	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.212 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.71	α = 90
b = 58.71	β = 90
c = 93.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): Krauchenco, S., Nagem, R.A.P., da Silva, J.A., Marangoni, S., Polikarpov, I.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance