4ESY | pdb_00004esy

Crystal Structure of the CBS Domain of CBS Domain Containing Membrane Protein from Sphaerobacter thermophilus

• PDB DOI: https://doi.org/10.2210/pdb4ESY/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Sphaerobacter thermophilus DSM 20745
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-23 Released: 2012-09-05 
• Deposition Author(s): Kim, Y., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal Structure of the CBS Domain of CBS Domain Containing Membrane Protein from Sphaerobacter thermophilus

Kim, Y., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.96 kDa 
• Atom Count: 2,871 
• Modeled Residue Count: 326 
• Deposited Residue Count: 340 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain containing membrane protein	A	170	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0  Gene Names: Sthe_3453
UniProt
Find proteins for D1CAK9 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1CAK9  Go to UniProtKB:  D1CAK9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain containing membrane protein	B	170	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0  Gene Names: Sthe_3453
UniProt
Find proteins for D1CAK9 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1CAK9  Go to UniProtKB:  D1CAK9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B	MET	Selenomethionine	C5 H11 N O2 Se
CSO	B	CYS	Hydroxylation	C3 H7 N O3 S

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34ESY

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.09	α = 90
b = 74.118	β = 99.13
c = 50.981	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Kim, Y., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary