7D6L | pdb_00007d6l

Crystal structure of Trx2 from D. radiodurans R1

PDB DOI: https://doi.org/10.2210/pdb7D6L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-30 Released: 2021-10-13
Deposition Author(s): Kim, M.-K., Zhang, J., Zhao, L.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.227 (Depositor), 0.227 (DCC)
R-Value Work:
0.191 (Depositor), 0.192 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7D6L

This is version 1.3 of the entry. See complete history.

Literature

Structural and Biochemical Characterization of Thioredoxin-2 from Deinococcus radiodurans.

Kim, M.-K., Zhao, L., Jeong, S., Zhang, J., Jung, J.-H., Seo, H.S., Choi, J.-, Lim, S.

(2021) Antioxidants (Basel) 10: 1843-1857

DOI: https://doi.org/10.3390/antiox10111843

Macromolecule Content

Total Structure Weight: 16.45 kDa
Atom Count: 1,162
Modeled Residue Count: 142
Deposited Residue Count: 148
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin 2	A	148	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0 Gene Names: DR_A0164
UniProt
Find proteins for Q9RYY9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RYY9 Go to UniProtKB: Q9RYY9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RYY9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.227 (Depositor), 0.227 (DCC)
R-Value Work: 0.191 (Depositor), 0.192 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.887	α = 90
b = 57.819	β = 94.78
c = 36.152	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2020R1F1A1057780

Revision History (Full details and data files)

Version 1.0: 2021-10-13
Type: Initial release
Version 1.1: 2021-12-01
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.