6N1N | pdb_00006n1n

Crystal structure of class D beta-lactamase from Sebaldella termitidis ATCC 33386

• PDB DOI: https://doi.org/10.2210/pdb6N1N/pdb

• Classification: HYDROLASE
• Organism(s): Sebaldella termitidis ATCC 33386
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-09 Released: 2018-12-19 
• Deposition Author(s): Michalska, K., Tesar, C., Endres, M., Joachimiak, A., Satchell, K.J., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Crystal structure of class D beta-lactamase from Sebaldella termitidis ATCC 33386

Michalska, K., Tesar, C., Endres, M., Joachimiak, A., Satchell, K.J., 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: 30.51 kDa 
• Atom Count: 2,434 
• Modeled Residue Count: 248 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	250	Sebaldella termitidis ATCC 33386	Mutation(s): 0  Gene Names: Sterm_0301 EC: 3.5.2.6
UniProt
Find proteins for D1ALR7 (Sebaldella termitidis (strain ATCC 33386 / NCTC 11300)) Explore D1ALR7  Go to UniProtKB:  D1ALR7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36n1n

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.51	α = 90
b = 97.546	β = 90
c = 40.328	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SBC-Collect	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Michalska, K., Tesar, C., Endres, M., Joachimiak, A., Satchell, K.J., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2025-04-02
  Changes: Data collection, Database references, Structure summary