4BEN

R39-imipenem Acyl-enzyme crystal structure

• PDB DOI: https://doi.org/10.2210/pdb4BEN/pdb

• Classification: HYDROLASE
• Organism(s): Actinomadura sp. R39
• Mutation(s): No 


• Deposited: 2013-03-11 Released: 2013-03-20 
• Deposition Author(s): Van Elder, D., Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.234 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Crystal Structures of R39-Imipenem Acyl-Enzyme.

Sauvage, E., Van Elder, D., Herman, R., Kerff, F., Pratt, R.F., Charlier, P.

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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 195.44 kDa 
• Atom Count: 14,637 
• Modelled Residue Count: 1,864 
• Deposited Residue Count: 1,864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE	A, B, C, D	466	Actinomadura sp. R39	Mutation(s): 0  EC: 3.4.16.4
UniProt
Find proteins for P39045 (Actinomadura sp. (strain R39)) Explore P39045  Go to UniProtKB:  P39045

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IM2	CA [auth C], E [auth A], KA [auth D], T [auth B]	(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid C12 H19 N3 O4 S UACUABDJLSUFFC-IWSPIJDZSA-N
MES	VA [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	AA [auth B], BA [auth B], DA [auth C], EA [auth C], FA [auth C], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], M [auth A], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], S [auth A], SA [auth D], TA [auth D], U [auth B], UA [auth D], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	L [auth A], RA [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	F [auth A], G [auth A], LA [auth D], MA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.234 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.623	α = 90
b = 91.911	β = 94.5
c = 106.924	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Van Elder, D., Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary
• Version 1.2: 2024-10-16
  Changes: Structure summary