7YKM | pdb_00007ykm

Structure of DciA DUF721 domain from Deinococcus radiodurans

PDB DOI: https://doi.org/10.2210/pdb7YKM/pdb

Classification: REPLICATION
Organism(s): Deinococcus radiodurans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-22 Released: 2023-08-02
Deposition Author(s): Cheng, K.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.215 (Depositor), 0.216 (DCC)
R-Value Work:
0.193 (Depositor), 0.193 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7YKM

This is version 1.1 of the entry. See complete history.

Literature

Structure of DciA DUF721 domain from Deinococcus radiodurans

Cheng, K.

To be published.

Macromolecule Content

Total Structure Weight: 11.65 kDa
Atom Count: 689
Modeled Residue Count: 81
Deposited Residue Count: 105
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DciA DUF721 domain	A	105	Deinococcus radiodurans	Mutation(s): 0 Gene Names: DR_1088
UniProt
Find proteins for Q9RVE1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RVE1 Go to UniProtKB: Q9RVE1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RVE1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.215 (Depositor), 0.216 (DCC)
R-Value Work: 0.193 (Depositor), 0.193 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.593	α = 90
b = 37.438	β = 164.339
c = 86.285	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100017

Revision History (Full details and data files)

Version 1.0: 2023-08-02
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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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.