5M85 | pdb_00005m85

Three-dimensional structure of the intermediate state of GAF3 from Slr1393 of Synechocystis sp. PCC6803

• PDB DOI: https://doi.org/10.2210/pdb5M85/pdb

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


• Deposited: 2016-10-28 Released: 2017-12-20 
• 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: 2.10 Å
• R-Value Free: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.170 (Depositor) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.9 kDa 
• Atom Count: 1,457 
• Modeled Residue Count: 159 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensory transduction 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC	B [auth A]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N
3CX	C [auth A]	(2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid C9 H19 N O4 S INEWUCPYEUEQTN-VIFPVBQESA-N
TRS	H [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
NA	D [auth A], E [auth A], F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.170 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.101	α = 90
b = 75.101	β = 90
c = 71.21	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Xu, X.-L., Zhao, K.-H., Gaertner, W., Hoeppner, A.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary