7ES4 | pdb_00007es4

the crystral structure of DndH-C-domain

  • 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 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.189 (Depositor) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7ES4

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 

Macromolecule Content 

  • Total Structure Weight: 43.81 kDa 
  • Atom Count: 3,141 
  • Modeled Residue Count: 373 
  • Deposited Residue Count: 375 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA phosphorothioation-dependent restriction protein DptH375Escherichia coliMutation(s): 0 
Gene Names: dptH

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.233 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.189 (Depositor) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.478α = 90
b = 102.478β = 90
c = 77.65γ = 120
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
AutoSolphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

  • Released Date: 2022-05-11 
    • Deposition Author(s): Wu, D.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31720103906

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
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary