3ICY | pdb_00003icy

The crystal structure of sensory box histidine kinase/response regulator domain from Chlorobium tepidum TLS

• PDB DOI: https://doi.org/10.2210/pdb3ICY/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Chlorobaculum tepidum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-19 Released: 2010-01-12 
• Deposition Author(s): Wu, R., Shonda, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.248 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.167 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: other

Literature

The crystal structure of sensory box histidine kinase/response regulator domain from Chlorobium

Ruiying, W., Shonda, C., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.17 kDa 
• Atom Count: 1,941 
• Modeled Residue Count: 236 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein	A, B	118	Chlorobaculum tepidum	Mutation(s): 0  Gene Names: CT2060, GI:21648093 EC: 2.7.13.3
UniProt
Find proteins for Q8KAU2 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)) Explore Q8KAU2  Go to UniProtKB:  Q8KAU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth B], F [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: 2.68 Å
• R-Value Free:  0.248 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.167 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.728	α = 90
b = 32.483	β = 114.67
c = 93.755	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MLPHARE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Wu, R., Shonda, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary