6N9K | pdb_00006n9k

Beta-lactamase from Escherichia coli str. Sakai

• PDB DOI: https://doi.org/10.2210/pdb6N9K/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-12-03 Released: 2018-12-12 
• Deposition Author(s): Osipiuk, J., Wu, R., Endres, M., Joachimiak, A., 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: 
  0.156 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

Beta-lactamase from Escherichia coli str. Sakai

Osipiuk, J., Wu, R., Endres, M., 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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 80.33 kDa 
• Atom Count: 6,645 
• Modeled Residue Count: 717 
• Deposited Residue Count: 722 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	361	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: ampC, ECpv15279_5067, ECs_5131 EC: 3.5.2.6
UniProt
Find proteins for Q8XDQ2 (Escherichia coli O157:H7) Explore Q8XDQ2  Go to UniProtKB:  Q8XDQ2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.156 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36n9k

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.929	α = 90
b = 127.929	β = 90
c = 93.02	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Osipiuk, J., Wu, R., Endres, M., Joachimiak, A., 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	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence, Other
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description