3KXR

Structure of the cystathionine beta-synthase pair domain of the putative Mg2+ transporter SO5017 from Shewanella oneidensis MR-1.

• PDB DOI: https://doi.org/10.2210/pdb3KXR/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-03 Released: 2009-12-15 
• Deposition Author(s): Fratczak, Z., Zimmerman, M.D., Chruszcz, M., Cymborowski, M., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Structure of the cystathionine beta-synthase pair domain of the putative Mg2+ transporter SO5017 from Shewanella oneidensis MR-1.

Fratczak, Z., Zimmerman, M.D., Chruszcz, M., Cymborowski, M., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 23.82 kDa 
• Atom Count: 1,396 
• Modelled Residue Count: 171 
• Deposited Residue Count: 205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnesium transporter, putative	A	205	Shewanella oneidensis MR-1	Mutation(s): 0  Gene Names: SO_1565
UniProt
Find proteins for Q8EGN5 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8EGN5  Go to UniProtKB:  Q8EGN5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.596	α = 90
b = 103.596	β = 90
c = 134.302	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
ARP/wARP	model building
CCP4	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-2000	data scaling
DM	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-15 
Deposition Author(s): Fratczak, Z., Zimmerman, M.D., Chruszcz, M., Cymborowski, M., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-06
  Changes: Data collection, Structure summary