8WJ5

Double-wing domain of E. coli YdcD

• PDB DOI: https://doi.org/10.2210/pdb8WJ5/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-25 Released: 2024-10-02 
• Deposition Author(s): Kamata, K., Tame, J.R.H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Starting Model: in silico

Literature

Making the unphasable feasible

Kamata, K., Tame, J.R.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 16.79 kDa 
• Atom Count: 1,233 
• Modelled Residue Count: 130 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YdcD	A	140	Escherichia coli K-12	Mutation(s): 0  Gene Names: ydcD
UniProt
Find proteins for P31991 (Escherichia coli (strain K12)) Explore P31991  Go to UniProtKB:  P31991

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.545	α = 90
b = 75.545	β = 90
c = 62.043	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Kamata, K., Tame, J.R.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary