3EMX | pdb_00003emx

Crystal structure of thioredoxin from Aeropyrum pernix

• PDB DOI: https://doi.org/10.2210/pdb3EMX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aeropyrum pernix
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-25 Released: 2008-10-14 
• Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Miller, S., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.254 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Crystal structure of thioredoxin from Aeropyrum pernix

Bonanno, J.B., Dickey, M., Bain, K.T., Miller, S., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.54 kDa 
• Atom Count: 1,996 
• Modeled Residue Count: 248 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin	A, B	135	Aeropyrum pernix	Mutation(s): 0  Gene Names: APE0641, APE_0641
UniProt
Find proteins for Q9YED4 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YED4  Go to UniProtKB:  Q9YED4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.254 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.229	α = 90
b = 54.852	β = 90
c = 159.342	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Miller, S., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references