7EXX | pdb_00007exx

The structure of DndG

PDB DOI: https://doi.org/10.2210/pdb7EXX/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-05-28 Released: 2022-06-01
Deposition Author(s): Wu, D., Wang, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.214 (Depositor), 0.189 (DCC)
R-Value Work:
0.166 (Depositor)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7EXX

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

Literature

The functional coupling between restriction and DNA phosphorothioate modification systems underlying the DndFGH restriction complex

Wu, D., Tang, Y., Chen, S., He, Y., Chang, X., Zheng, W., Deng, Z., Li, Z., Wang, L., Wu, G., Chen, S.

(2022) Nat Catal

DOI: https://doi.org/10.1038/s41929-022-00884-2

Macromolecule Content

Total Structure Weight: 51.79 kDa
Atom Count: 3,701
Modeled Residue Count: 440
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA phosphorothioation-dependent restriction protein DptG	A	444	Escherichia coli	Mutation(s): 0 Gene Names: dptG
UniProt
Find proteins for A0A0P7R7Y1 (Escherichia coli) Explore A0A0P7R7Y1 Go to UniProtKB: A0A0P7R7Y1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0P7R7Y1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA (Subject of Investigation/LOI) Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSP Query on CSP	A	L-PEPTIDE LINKING	C₃ H₈ N O₅ P S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.214 (Depositor), 0.189 (DCC)
R-Value Work: 0.166 (Depositor)
R-Value Observed: 0.168 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.248	α = 90
b = 182.286	β = 90
c = 59.492	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31720103906

Revision History (Full details and data files)

Version 1.0: 2022-06-01
Type: Initial release
Version 1.1: 2022-12-14
Changes: Database references, Structure summary
Version 1.2: 2022-12-21
Changes: Database references, Structure summary
Version 1.3: 2024-11-13
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.