6NFD

beta-lactamase SHV-11 from Klebsiella pneumoniae strain NTUH-K2044

• PDB DOI: https://doi.org/10.2210/pdb6NFD/pdb

• Classification: LIGASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-12-19 Released: 2018-12-26 
• Deposition Author(s): Osipiuk, J., Welk, L., 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 0.135 
• R-Value Work: 0.118 
• R-Value Observed: 0.119 

Starting Model: experimental

Literature

beta-lactamase SHV-11 from Klebsiella pneumoniae strain NTUH-K2044

Osipiuk, J., Welk, L., 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)

Macromolecule Content

• Total Structure Weight: 29.81 kDa 
• Atom Count: 2,628 
• Modelled Residue Count: 267 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-lactamase SHV-11	A	268	Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044	Mutation(s): 0  Gene Names: blaSHV-11 EC: 3.5.2.6
UniProt
Find proteins for A0A4P1LYI7 (Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044) Explore A0A4P1LYI7  Go to UniProtKB:  A0A4P1LYI7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.17 Å
• R-Value Free: 0.135 
• R-Value Work: 0.118 
• R-Value Observed: 0.119 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/m36nfd

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.158	α = 90
b = 123.543	β = 90
c = 124.48	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Osipiuk, J., Welk, L., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

---

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: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Structure summary