5HPA

The crystal of rhodanese domain of YgaP treated with sodium thiosulfate

• PDB DOI: https://doi.org/10.2210/pdb5HPA/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-20 Released: 2017-02-01 
• Deposition Author(s): Eichmann, C., Tzitzilonis, C., Kwiatkowski, W., Riek, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.197 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

S-Sulfhydration of the Catalytic Cysteine in the Rhodanese Domain of YgaP is a Complex Dynamical Process.

Eichmann, C., Tzitzilonis, C., Kwiatkowski, W., Riek, R.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 14.08 kDa 
• Atom Count: 998 
• Modelled Residue Count: 104 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inner membrane protein YgaP	A	127	Escherichia coli K-12	Mutation(s): 0  Gene Names: ygaP, b2668, JW2643
UniProt
Find proteins for P55734 (Escherichia coli (strain K12)) Explore P55734  Go to UniProtKB:  P55734

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.197 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.699	α = 90
b = 43.699	β = 90
c = 52.28	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Eichmann, C., Tzitzilonis, C., Kwiatkowski, W., Riek, R.

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description