6WUE | pdb_00006wue

Tetragonal crystal form of SbtB from Synechocystis PCC6803

• PDB DOI: https://doi.org/10.2210/pdb6WUE/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Synechocystis sp. PCC 6803
• Expression System: Escherichia coli BW25113
• Mutation(s): No 


• Deposited: 2020-05-04 Released: 2020-08-26 
• Deposition Author(s): Bu, G., Simmons, C.R., Nielsen, D.R., Nannenga, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Tetragonal crystal form of the cyanobacterial bicarbonate-transporter regulator SbtB from Synechocystis sp. PCC 6803.

Bu, G., Simmons, C.R., Nielsen, D.R., Nannenga, B.L.

(2020) Acta Crystallogr F Struct Biol Commun 76: 438-443

• PubMed: 32880592 
• DOI: https://doi.org/10.1107/S2053230X20010523
• Primary Citation Related Structures: 
  6WUE


• PubMed Abstract: 
  

  The P _II -like protein SbtB has been identified as a regulator of SbtA, which is one of the key bicarbonate transporters in cyanobacteria. While SbtB from Synechocystis sp. PCC 6803 has previously been shown to be a trimer, a new crystal form is reported here which crystallizes in what is thought to be a non-native tetramer in the crystal, with the C-terminus in an extended conformation. The crystal structure shows the formation of an intermolecular disulfide bond at Cys94 between SbtB monomers, which may stabilize this conformation in the crystal. This motivates the need for future studies to investigate the potential role that the oxidation and reduction of these cysteines may play in the activation and/or function of SbtB.

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Organizational Affiliation: 
• Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA.
Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 24.19 kDa 
• Atom Count: 1,564 
• Modeled Residue Count: 177 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-associated protein slr1513	A, B	110	Synechocystis sp. PCC 6803	Mutation(s): 0  Gene Names: slr1513
UniProt
Find proteins for P73954 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73954  Go to UniProtKB:  P73954

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA (Subject of Investigation/LOI)	C [auth B], D [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.571	α = 90
b = 51.571	β = 90
c = 178.412	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Bu, G., Simmons, C.R., Nielsen, D.R., Nannenga, B.L.

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2020-09-16
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary