6EJP | pdb_00006ejp

Yersinia YscU C-terminal fragment in complex with a synthetic compound

• PDB DOI: https://doi.org/10.2210/pdb6EJP/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-22 Released: 2018-10-10 
• Deposition Author(s): Karlberg, T., Thorsell, A.G., Ho, O., Sunduru, N., Elofsson, M., Wolf-Watz, M., Schuler, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Yersinia YscU C-terminal fragment in complex with a synthetic compound

Karlberg, T., Thorsell, A.G., Ho, O., Sunduru, N., Elofsson, M., Wolf-Watz, M., Schuler, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.6 kDa 
• Atom Count: 2,391 
• Modeled Residue Count: 281 
• Deposited Residue Count: 298 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Yop proteins translocation protein U	A, C [auth B]	58	Yersinia pestis	Mutation(s): 0  Gene Names: yscU, YPCD1.47, y5031, y0034, YP_pCD36
UniProt
Find proteins for P69986 (Yersinia pestis) Explore P69986  Go to UniProtKB:  P69986

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Yop proteins translocation protein U	B [auth C], D	91	Yersinia pestis	Mutation(s): 0  Gene Names: yscU, YPCD1.47, y5031, y0034, YP_pCD36
UniProt
Find proteins for P69986 (Yersinia pestis) Explore P69986  Go to UniProtKB:  P69986

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B8E	G [auth C], K [auth D]	methyl 2-(5-methyl-2-phenyl-1,3-thiazol-4-yl)ethanoate C13 H13 N O2 S IGRGQWSVDTYHID-UHFFFAOYSA-N
PO4	E [auth A], H [auth C], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	I [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.74	α = 90
b = 69.65	β = 90
c = 242.67	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Karlberg, T., Thorsell, A.G., Ho, O., Sunduru, N., Elofsson, M., Wolf-Watz, M., Schuler, H.

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary