4ER9 | pdb_00004er9

Crystal structure of cytochrome b562 from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

• PDB DOI: https://doi.org/10.2210/pdb4ER9/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-19 Released: 2012-05-09 
• Deposition Author(s): Tan, K., Hatzos-Skintges, C., Jedrzejczak, R., Adkins, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Crystal structure of cytochrome b562 from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Tan, K., Hatzos-Skintges, C., Jedrzejczak, R., Adkins, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 14.69 kDa 
• Atom Count: 862 
• Modeled Residue Count: 105 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A	131	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: cybC, STM4439
UniProt
Find proteins for P63727 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P63727  Go to UniProtKB:  P63727

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.388	α = 90
b = 67.388	β = 90
c = 57.189	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Tan, K., Hatzos-Skintges, C., Jedrzejczak, R., Adkins, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations