5UBU | pdb_00005ubu

2.75 Angstrom Resolution Crystal Structure of Acetamidase from Yersinia enterocolitica.

• PDB DOI: https://doi.org/10.2210/pdb5UBU/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia enterocolitica subsp. palearctica Y11
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-21 Released: 2017-01-04 
• Deposition Author(s): Minasov, G., Shuvalova, L., Flores, K., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

2.75 Angstrom Resolution Crystal Structure of Acetamidase from Yersinia enterocolitica.

Minasov, G., Shuvalova, L., Flores, K., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 149.69 kDa 
• Atom Count: 10,660 
• Modeled Residue Count: 1,320 
• Deposited Residue Count: 1,328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acetamidase/formamidase	A, B, C, D	332	Yersinia enterocolitica subsp. palearctica Y11	Mutation(s): 0  Gene Names: Y11_22331
UniProt
Find proteins for A0A0H3NNJ4 (Yersinia enterocolitica subsp. palearctica serotype O:3 (strain DSM 13030 / CIP 106945 / Y11)) Explore A0A0H3NNJ4  Go to UniProtKB:  A0A0H3NNJ4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35ubu

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.884	α = 90
b = 137.884	β = 90
c = 204.281	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-04 
Deposition Author(s): Minasov, G., Shuvalova, L., Flores, K., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2017-01-04
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary