5FQ1 | pdb_00005fq1

Structure of the cytoplasmic PAS domain of the Geobacillus thermodenitrificans histidine kinase CitA

• PDB DOI: https://doi.org/10.2210/pdb5FQ1/pdb

• Classification: TRANSFERASE
• Organism(s): Geobacillus thermodenitrificans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-03 Released: 2017-01-11 
• Deposition Author(s): Schomburg, B., Giller, K., Becker, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.216 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Cryogenic optical localization provides 3D protein structure data with Angstrom resolution.

Weisenburger, S., Boening, D., Schomburg, B., Giller, K., Becker, S., Griesinger, C., Sandoghdar, V.

(2017) Nat Methods 14: 141-144

• PubMed: 28068317 
• DOI: https://doi.org/10.1038/nmeth.4141
• Primary Citation Related Structures: 
  5FQ1


• PubMed Abstract: 
  

  We introduce Cryogenic Optical Localization in 3D (COLD), a method to localize multiple fluorescent sites within a single small protein with Angstrom resolution. We demonstrate COLD by determining the conformational state of the cytosolic Per-ARNT-Sim domain from the histidine kinase CitA of Geobacillus thermodenitrificans and resolving the four biotin sites of streptavidin. COLD provides quantitative 3D information about small- to medium-sized biomolecules on the Angstrom scale and complements other techniques in structural biology.

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Organizational Affiliation: 
• Max Planck Institute for the Science of Light, Erlangen, Germany.
Department of Physics, Friedrich Alexander University (FAU) Erlangen-Nürnberg, Erlangen, Germany.
Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 25.54 kDa 
• Atom Count: 1,796 
• Modeled Residue Count: 221 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTIDINE KINASE	A, B	112	Geobacillus thermodenitrificans	Mutation(s): 0  EC: 2.7.13.3
UniProt
Find proteins for A4IPE6 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4IPE6  Go to UniProtKB:  A4IPE6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], D [auth A], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.216 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.453	α = 90
b = 74.036	β = 90
c = 75.081	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
SHELXCD	phasing
SHELXD	phasing
SHELXE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Schomburg, B., Giller, K., Becker, S.

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-03-01
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary