5V4F | pdb_00005v4f

Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family YyfB from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb5V4F/pdb

• Classification: Structural genomics, unknown function
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-09 Released: 2017-04-05 
• Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Krishnan, A., Babnigg, G., Schneewind, O., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.200 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family YyfB from Yersinia pestis

Kim, Y., Chhor, G., Endres, M., Krishnan, A., Babnigg, G., Schneewind, O., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 30.31 kDa 
• Atom Count: 2,143 
• Modeled Residue Count: 266 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative translational inhibitor protein	A, B	137	Yersinia pestis	Mutation(s): 0  Gene Names: tdcF4, y3550, YP_2945, YPO0628
UniProt
Find proteins for A0A3N4B9A3 (Yersinia pestis) Explore A0A3N4B9A3  Go to UniProtKB:  A0A3N4B9A3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 3.00 Å
• R-Value Free:  0.200 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.205	α = 90
b = 129.205	β = 90
c = 129.205	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Krishnan, A., Babnigg, G., Schneewind, O., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary