4E29 | pdb_00004e29

Periplasmic domain of the chimeric WzzB chain length regulator protein

• PDB DOI: https://doi.org/10.2210/pdb4E29/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Shigella flexneri, Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-07 Released: 2012-03-28 
• Deposition Author(s): Kalynych, S., Yao, D., Magee, J.D., Cygler, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Structural Characterization of Closely Related O-antigen Lipopolysaccharide (LPS) Chain Length Regulators.

Kalynych, S., Yao, D., Magee, J., Cygler, M.

(2012) J Biological Chem 287: 15696-15705

• PubMed: 22437828 
• DOI: https://doi.org/10.1074/jbc.M112.354837
• Primary Citation Related Structures: 
  4E29, 4E2C, 4E2H, 4E2L


• PubMed Abstract: 
  

  The surface O-antigen polymers of gram-negative bacteria exhibit a modal length distribution that depends on dedicated chain length regulator periplasmic proteins (polysaccharide co-polymerases, PCPs) anchored in the inner membrane by two transmembrane helices. In an attempt to determine whether structural changes underlie the O-antigen modal length specification, we have determined the crystal structures of several closely related PCPs, namely two chimeric PCP-1 family members solved at 1.6 and 2.8 Å and a wild-type PCP-1 from Shigella flexneri solved at 2.8 Å. The chimeric proteins form circular octamers, whereas the wild-type WzzB from S. flexneri was found to be an open trimer. We also present the structure of a Wzz(FepE) mutant, which exhibits severe attenuation in its ability to produce very long O-antigen polymers. Our findings suggest that the differences in the modal length distribution depend primarily on the surface-exposed amino acids in specific regions rather than on the differences in the oligomeric state of the PCP protomers.

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Organizational Affiliation: 
• Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C8  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 56.65 kDa 
• Atom Count: 4,304 
• Modeled Residue Count: 463 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric WzzB chain length determinant protein	A, B	248	Shigella flexneri, Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 This entity is chimeric	Mutation(s): 0  Gene Names: cld, rol, S2210, SF2089, wzzB, STM2079
UniProt
Find proteins for P37792 (Shigella flexneri) Explore P37792  Go to UniProtKB:  P37792
Find proteins for Q04866 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q04866  Go to UniProtKB:  Q04866
UniProt Groups	P37792Q04866

Small Molecules

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: 1.60 Å
• R-Value Free:  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.757	α = 90
b = 115.757	β = 90
c = 210.885	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-3000	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Kalynych, S., Yao, D., Magee, J.D., Cygler, M.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Database references
• Version 1.2: 2012-06-20
  Changes: Database references
• Version 1.3: 2017-07-05
  Changes: Source and taxonomy
• Version 1.4: 2017-11-15
  Changes: Refinement description
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary