1X0R | pdb_00001x0r

Thioredoxin Peroxidase from Aeropyrum pernix K1

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

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

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

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable peroxiredoxin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
249Aeropyrum pernix K1Mutation(s): 5 
Gene Names: APE2278
EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for Q9Y9L0 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9Y9L0 
Go to UniProtKB:  Q9Y9L0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y9L0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO


Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth C]
AC [auth E]
AD [auth H]
AE [auth J]
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
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.171 (Depositor) 
  • R-Value Work:  0.164 (Depositor) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.633α = 105.37
b = 101.792β = 105.28
c = 102.886γ = 93.32
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-10-16
    Changes: Data collection, Structure summary