4E2G | pdb_00004e2g

Crystal structure of Cupin fold protein Sthe2323 from Sphaerobacter thermophilus

• PDB DOI: https://doi.org/10.2210/pdb4E2G/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Sphaerobacter thermophilus DSM 20745
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-08 Released: 2012-03-21 
• Deposition Author(s): Chang, C., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.211 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal structure of Cupin fold protein Sthe2323 from Sphaerobacter thermophilus

Chang, C., Hatzos-Skintges, C., Jedrzejczak, R., 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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 116.08 kDa 
• Atom Count: 8,241 
• Modelled Residue Count: 931 
• Deposited Residue Count: 1,008 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin 2 conserved barrel domain protein	A, B, C, D, E, F, G, H	126	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0  Gene Names: Sthe_2323
UniProt
Find proteins for D1C798 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C798  Go to UniProtKB:  D1C798

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	M [auth F]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI	I [auth B], J [auth C], L [auth F], N [auth G]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
K	K [auth C], O [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.211 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34E2G

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.71	α = 90
b = 52.623	β = 91.24
c = 108.818	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Chang, C., Hatzos-Skintges, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary