6MUQ

1.67 Angstrom Resolution Crystal Structure of Murein-DD-endopeptidase from Yersinia enterocolitica.

• PDB DOI: https://doi.org/10.2210/pdb6MUQ/pdb

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


• Deposited: 2018-10-23 Released: 2018-10-31 
• Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.204 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

1.67 Angstrom Resolution Crystal Structure of Murein-DD-endopeptidase from Yersinia enterocolitica.

Minasov, G., Shuvalova, L., Kiryukhina, O., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 31.75 kDa 
• Atom Count: 2,353 
• Modelled Residue Count: 267 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Murein-DD-endopeptidase	A	283	Yersinia enterocolitica subsp. palearctica Y11	Mutation(s): 0  Gene Names: Y11_17941
UniProt
Find proteins for A0A0H3NPR7 (Yersinia enterocolitica subsp. palearctica serotype O:3 (strain DSM 13030 / CIP 106945 / Y11)) Explore A0A0H3NPR7  Go to UniProtKB:  A0A0H3NPR7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.204 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m36muq

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.201	α = 90
b = 37.858	β = 115.75
c = 59.577	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection