6AZI

1.75 Angstrom Resolution Crystal Structure of D-alanyl-D-alanine Endopeptidase from Enterobacter cloacae in Complex with Covalently Bound Boronic Acid

• PDB DOI: https://doi.org/10.2210/pdb6AZI/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacter cloacae subsp. cloacae ATCC 13047
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-11 Released: 2017-10-04 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., 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: 1.75 Å
• R-Value Free: 0.238 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

1.75 Angstrom Resolution Crystal Structure of D-alanyl-D-alanine Endopeptidase from Enterobacter cloacae in Complex with Covalently Bound Boronic Acid.

Minasov, G., Wawrzak, Z., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A.

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: 31.94 kDa 
• Atom Count: 2,316 
• Modelled Residue Count: 252 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl-D-alanine endopeptidase	A	285	Enterobacter cloacae subsp. cloacae ATCC 13047	Mutation(s): 0  Gene Names: ECL_03445
UniProt
Find proteins for A0A0H3CN11 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56)) Explore A0A0H3CN11  Go to UniProtKB:  A0A0H3CN11

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BO4	B [auth A]	BORATE ION B H4 O4 KCFLOKKYWBPKFN-UHFFFAOYSA-N

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: 1.75 Å
• R-Value Free: 0.238 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M36AZI

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.47	α = 90
b = 64.233	β = 90
c = 79.519	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-04 
Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2017-10-04
  Type: Initial release
  
• Version 2.0: 2023-05-31
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary