7ES4

the crystral structure of DndH-C-domain

PDB DOI: https://doi.org/10.2210/pdb7ES4/pdb

Classification: TRANSLOCASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-05-08 Released: 2022-05-11
Deposition Author(s): Wu, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.233
R-Value Work: 0.189
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

This is version 1.2 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: 43.81 kDa
Atom Count: 3,141
Modelled Residue Count: 373
Deposited Residue Count: 375
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA phosphorothioation-dependent restriction protein DptH	A	375	Escherichia coli	Mutation(s): 0 Gene Names: dptH
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.233
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.478	α = 90
b = 102.478	β = 90
c = 77.65	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-11

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: 2022-05-11
Type: Initial release
Version 1.1: 2022-12-14
Changes: Database references
Version 1.2: 2022-12-21
Changes: Database references, Structure summary

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 R01GM133198.