7DKA | pdb_00007dka

Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, C24S mutant protein

PDB DOI: https://doi.org/10.2210/pdb7DKA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-11-23 Released: 2021-11-24
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: 1.56 Å
R-Value Free:
0.180 (Depositor), 0.180 (DCC)
R-Value Work:
0.155 (Depositor), 0.156 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, native protein

Kim, M.-K., Zhang, J., Zhao, L.

To be published.

Macromolecule Content

Total Structure Weight: 53.75 kDa
Atom Count: 3,987
Modeled Residue Count: 421
Deposited Residue Count: 464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DSBA domain-containing protein	A, B	232	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 1 Gene Names: DR_2335
UniProt
Find proteins for Q9RRZ4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RRZ4 Go to UniProtKB: Q9RRZ4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9RRZ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth B]	D [auth A], P [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain P [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain O [auth B] SDF format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] mmCIF format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A]	F [auth A], J [auth A], O [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain O [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	C [auth A] E [auth A] G [auth A] H [auth A] I [auth A] C [auth A], E [auth A], G [auth A], H [auth A], I [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.180 (Depositor), 0.180 (DCC)
R-Value Work: 0.155 (Depositor), 0.156 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.084	α = 90
b = 84.177	β = 91.54
c = 63.898	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-11-24

Deposition Author(s):

Kim, M.-K.

Zhang, J.

Zhao, L.

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: 2021-11-24
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 2.0: 2025-09-17
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary