5DFY

Structure of the parental state of GAF3 from Slr1393 of Synechocystis sp. PCC6803 (in vitro assembled protein/chromophore)

• PDB DOI: https://doi.org/10.2210/pdb5DFY/pdb

• Classification: TRANSFERASE
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-27 Released: 2016-09-14 
• Deposition Author(s): Xu, X.-L., Zhao, K.-H., Gaertner, W., Hoeppner, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.181 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Literature

Structural elements regulating the photochromicity in a cyanobacteriochrome

Xu, X.-L., Hoeppner, A., Wiebeler, C., Zhao, K.-H., Schapiro, I., Gaertner, W.

(2020) Proc Natl Acad Sci U S A 

• DOI: https://doi.org/10.1073/pnas.1910208117

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.45 kDa 
• Atom Count: 1,581 
• Modelled Residue Count: 158 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine kinase	A	215	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: slr1393 EC: 2.7.13.3
UniProt
Find proteins for P73184 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73184  Go to UniProtKB:  P73184

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC	B [auth A]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.181 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.94	α = 90
b = 62.94	β = 90
c = 119.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Xu, X.-L., Zhao, K.-H., Gaertner, W., Hoeppner, A.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 2.0: 2020-01-29
  Changes: Atomic model, Database references
• Version 2.1: 2024-10-16
  Changes: Data collection, Database references, Structure summary