1X0R

Thioredoxin Peroxidase from Aeropyrum pernix K1

• PDB DOI: https://doi.org/10.2210/pdb1X0R/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-03-28 Released: 2005-12-20 
• Deposition Author(s): Nakamura, T., Yamamoto, T., Inoue, T., Matsumura, H., Kobayashi, A., Hagihara, Y., Uegaki, K., Ataka, M., Kai, Y., Ishikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.171 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 

Literature

Crystal structure of thioredoxin peroxidase from aerobic hyperthermophilic archaeon Aeropyrum pernix K1

Nakamura, T., Yamamoto, T., Inoue, T., Matsumura, H., Kobayashi, A., Hagihara, Y., Uegaki, K., Ataka, M., Kai, Y., Ishikawa, K.

(2006) Proteins 62: 822-826

• PubMed: 16342268 
• DOI: https://doi.org/10.1002/prot.20796
• Primary Citation of Related Structures:  
  1X0R

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Organizational Affiliation: 

National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 6 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 295.79 kDa 
• Atom Count: 21,431 
• Modelled Residue Count: 2,440 
• Deposited Residue Count: 2,490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable peroxiredoxin	A, B, C, D, E, F, G, H, I, J	249	Aeropyrum pernix K1	Mutation(s): 5  Gene Names: APE2278 EC: 1.11.1.15
UniProt
Find proteins for Q9Y9L0 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9Y9L0  Go to UniProtKB:  Q9Y9L0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	AA [auth B], AB [auth C], AC [auth E], AD [auth H], AE [auth J], BA [auth B], BB [auth C], BC [auth E], BD [auth H], BE [auth J], CA [auth B], CB [auth D], CC [auth E], CD [auth H], CE [auth J], DA [auth B], DB [auth D], DC [auth F], DD [auth H], DE [auth J], EA [auth B], EB [auth D], EC [auth F], ED [auth H], EE [auth J], FA [auth B], FB [auth D], FC [auth F], FD [auth H], FE [auth J], GA [auth B], GB [auth D], GC [auth F], GD [auth H], GE [auth J], HA [auth B], HB [auth D], HC [auth F], HD [auth I], HE [auth J], IA [auth B], IB [auth D], IC [auth F], ID [auth I], JA [auth B], JB [auth D], JC [auth F], JD [auth I], K [auth A], KA [auth B], KB [auth D], KC [auth F], KD [auth I], L [auth A], LA [auth B], LB [auth D], LC [auth F], LD [auth I], M [auth A], MA [auth C], MB [auth E], MC [auth F], MD [auth I], N [auth A], NA [auth C], NB [auth E], NC [auth F], ND [auth I], O [auth A], OA [auth C], OB [auth E], OC [auth F], OD [auth I], P [auth A], PA [auth C], PB [auth E], PC [auth G], PD [auth I], Q [auth A], QA [auth C], QB [auth E], QC [auth G], QD [auth I], R [auth A], RA [auth C], RB [auth E], RC [auth G], RD [auth I], S [auth A], SA [auth C], SB [auth E], SC [auth G], SD [auth J], T [auth A], TA [auth C], TB [auth E], TC [auth G], TD [auth J], U [auth A], UA [auth C], UB [auth E], UC [auth G], UD [auth J], V [auth A], VA [auth C], VB [auth E], VC [auth G], VD [auth J], W [auth A], WA [auth C], WB [auth E], WC [auth G], WD [auth J], X [auth A], XA [auth C], XB [auth E], XC [auth G], XD [auth J], Y [auth B], YA [auth C], YB [auth E], YC [auth H], YD [auth J], Z [auth B], ZA [auth C], ZB [auth E], ZC [auth H], ZD [auth J]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.171 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.633	α = 105.37
b = 101.792	β = 105.28
c = 102.886	γ = 93.32

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-20 
Deposition Author(s): Nakamura, T., Yamamoto, T., Inoue, T., Matsumura, H., Kobayashi, A., Hagihara, Y., Uegaki, K., Ataka, M., Kai, Y., Ishikawa, K.

Revision History  

• Version 1.0: 2005-12-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations