3T1U

Crystal Structure of the complex of Cyclophilin-A enzyme from Azotobacter vinelandii with sucAFPFpNA peptide

• PDB DOI: https://doi.org/10.2210/pdb3T1U/pdb

• Classification: ISOMERASE
• Organism(s): Azotobacter vinelandii DJ
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-07-22 Released: 2012-03-07 
• Deposition Author(s): Karpusas, M., Christoforides, E., Bethanis, K., Dimou, M., Katinakis, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Structure of a bacterial cytoplasmic cyclophilin A in complex with a tetrapeptide.

Christoforides, E., Dimou, M., Katinakis, P., Bethanis, K., Karpusas, M.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 259-264

• PubMed: 22442217 
• DOI: https://doi.org/10.1107/S1744309112000188
• Primary Citation of Related Structures:  
  3T1U


• PubMed Abstract: 
  

  Cyclophilins constitute a class of peptidyl-prolyl isomerases which participate in processes related to protein folding, signalling and chaperoning. The crystal structure of the cytoplasmic cyclophilin A (CyPA) from the bacterium Azotobacter vinelandii complexed with a synthetic tetrapeptide was determined by molecular replacement at 2 resolution. The proline in the tetrapeptide is observed to adopt the cis-isomer conformation. Comparisons of this structure with other CyPA structures provide insights into the conformational variability, effects of peptide binding and structure-function relationships of this enzyme.

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Organizational Affiliation: 

Physics Laboratory, Department of Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.38 kDa 
• Atom Count: 1,414 
• Modelled Residue Count: 169 
• Deposited Residue Count: 169 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A	163	Azotobacter vinelandii DJ	Mutation(s): 0  Gene Names: Avin_23510 EC: 5.2.1.8
UniProt
Find proteins for C1DHE4 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DHE4  Go to UniProtKB:  C1DHE4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
succinyl-Ala-Phe-Pro-Phe-p-nitroanilide	B	6	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.41	α = 90
b = 66.41	β = 90
c = 71.53	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
Deposition Author(s): Karpusas, M., Christoforides, E., Bethanis, K., Dimou, M., Katinakis, P.

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2013-01-23
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Refinement description