5TFQ | pdb_00005tfq

Crystal structure of a representative of class A beta-lactamase from Bacteroides cellulosilyticus DSM 14838

• PDB DOI: https://doi.org/10.2210/pdb5TFQ/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides cellulosilyticus DSM 14838
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-26 Released: 2016-11-02 
• Deposition Author(s): Nocek, B., Hatzos-Skintges, C., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 
  0.134 (Depositor), 0.139 (DCC) 
• R-Value Work: 
  0.115 (Depositor), 0.121 (DCC) 
• R-Value Observed: 
  0.116 (Depositor) 

Literature

Crystal structure of a representative of class A beta-lactamase from Bacteroides cellulosilyticus DSM 14838

Nocek, B., Hatzos-Skintges, C., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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: 31.45 kDa 
• Atom Count: 2,664 
• Modelled Residue Count: 277 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	280	Bacteroides cellulosilyticus DSM 14838	Mutation(s): 0  Gene Names: BACCELL_03967 EC: 3.5.2.6
UniProt
Find proteins for E2NI36 (Bacteroides cellulosilyticus DSM 14838) Explore E2NI36  Go to UniProtKB:  E2NI36

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.07 Å
• R-Value Free:  0.134 (Depositor), 0.139 (DCC) 
• R-Value Work:  0.115 (Depositor), 0.121 (DCC) 
• R-Value Observed: 0.116 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.837	α = 90
b = 62.808	β = 90
c = 87.058	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Nocek, B., Hatzos-Skintges, C., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary